Functional marker development of miR1511-InDel and allelic diversity within the genus Glycine.

BACKGROUND: Single-stranded non-protein coding small RNAs, 18-25 nucleotides in length, are ubiquitous throughout plants genomes and are involved in post-transcriptional gene regulation. Several types of DNA markers have been reported for the detection of genetic diversity or sequence variation in soybean, one of the most important legume crops in worldwide for seed protein and oil content. Recently, with the available of public genomic databases, there has been a shift from the labor-intensive development of PCR-based markers to sequence-based genotyping and the development of functional markers within genes, often coupled with the use of RNA information. But thus far miRNA-based markers have been only developed in rice and tobacco. Here we report the first functional molecular miRNA marker, miR1511-InDel, in soybean for a specific single copy locus used to assess genetic variation in domesticated soybean (Glycine max [L.] Merr) and its wild progenitor (Glycine soja Sieb. & Zucc.). RESULTS: We genotyped a total of 1,669 accessions of domesticated soybean (G. max) and its wild progenitor G. soja which are native throughout the China and parts of Korea, Japan and Russia. The results indicate that the miR1511 locus is distributed in cultivated soybean and has three alleles in annual wild soybean. Based on this result, we proposed that miR-InDel marker technology can be used to assess genetic variation. The inclusion of geo-reference data with miR1511-InDel marker data corroborated that accessions from the Yellow River basin (Huanghuai) exhibited high genetic diversity which provides more molecular evidence for gene diversity in annual wild soybean and domestication of soybean. CONCLUSIONS: These results provide evidence for the use of RNA marker, miRNA1511-InDel, as a soybean-specific functional maker for the study of genetic diversity, genotyping of germplasm and evolution studies. This is also the first report of functional marker developed from soybean miRNA located within the functional region of pre-miRNA1511.

[Diagnostic value of anti-alpha-fodrin antibody testing for Sjögren's syndrome: a meta-analysis].

OBJECTIVE: To evaluate the diagnostic accuracy of anti-alpha-fodrin antibody for Sjögren's syndrome (SS). METHODS: Qualified literatures on evaluation of anti-alpha-fodrin antibody in diagnosis of SS in English and Chinese published between January 1997 and December 2007 were retrieved from the Cochrane Library, Medline, Embase, and China National Knowledge Infrastructure (CNKI) databases, etc. Two reviewers independently assessed the methodological quality of each study with the tool QUADAS (quality assessment of diagnostic accuracy studies). Statistical analysis was performed by employing MATLAB, Review Manager 4.2 and Meta-Disc1.4. A meta-analysis of the reported sensitivity and specificity of each study and Summary Receiver Operating Characteristic (SROC) curve was performed. RESULTS: Eighteen literatures were included at last. After testing the heterogeneity of the included articles, proper effect model was selected to calculate the pooled weighted sensitivity and specificity with 95% confidence interval: for anti-alpha-fodrin antibody IgG, the sensitivity was 0.40 [95%CI (0.37-0.43)] and the specificity was 0.82 [95%CI (0.79-0.84)], the area under the curve (AUC) of SROC was 0.8029 (SE=0.0580). Eight studies tested anti-alpha-fodrin antibody IgA, the pooled weighted sensitivity and specificity with 95% confidence interval were 0.34 [95%CI (0.30-0.38)] and 0.83 [95%CI (0.79-0.86)] respectively, the AUC of SROC was 0.6374 (SE=0.1841), the synthesis data all showed heterogeneity. The subgroups were analyzed to identify the sources of heterogeneity according to age, race, assay method, agent source, diagnostic criteria, and country. There was homogeneity among the 4 studies from China, and the 6 studies from Japan, the AUC of SROC were 0.7343 (SE=0.0448) and 0.9273 (SE=0.0394), respectively. CONCLUSION: Diagnostic criteria, agent source, assay method, age, race, and country are the important sources of heterogeneity. Anti-alpha-fodrin antibodies IgG and IgA have relatively low pooled sensitivity and relatively high pooled specificity. Negative anti-alpha-fodrin antibody has not important value in excluding SS, but positive anti-alpha-fodrin antibody may be a useful parameter in clinical diagnosis of SS.

[Diagnostic value of anti-cyclic citrullinated peptide antibody for rheumatoid arthritis: a meta-analysis].

OBJECTIVE: To evaluate the diagnostic value of anti-cyclic citrullinated peptide (CCP) antibody for rheumatoid arthritis. METHODS: Data about RA from January 2000 to December 2005 were retrieved through Cochrane Library, Pubmed database, Excerpta Medica Database (EMBASE), OVID database, and China National Knowledge Infrastructure (CNKI), especially through the Annul of the Rheumatic Disease and relevant gray literatures, by entering the words "cyclic citrullinated peptides", "rheumatoid arthritis", "sensitivity", and "specificity". The inclusion of qualified literatures was based on the criteria for diagnostic research recommended by the Cochrane Methods Group on Screening and Diagnostic Test. Statistical analysis wes performed by employing the softwares of MATLAB and Review Manager 4, 2, and summary receiver operation characteristic (SROC) curve method. RESULTS: Twenty-two articles, 15 in English and 7 in Chinese, were extracted. The reported sensitivity of anti-CCP for the diagnosis of RA ranged from 39.2% to 84.6%, and the reported specificity ranged from 90% to 97.9%. The heterogeneity of the included articles was tested, a proper effect model was selected to calculate the pooled weighted sensitivity and specificity with 95% confidence interval for anti-CCP antibody as 77.3% (63.1%, 89.2%) and 93.85% (85.5%, 98.1%), and the positive and negative likelihood ratios as 12.0 and 0.24 respectively. The area under the curve of SROC was 0.8976, and the Q value was 0.87. The sensitivity of the patients with the duration of illness < 1 year was 43%, significantly lower than that of the patients with a duration of illness > 1 year (70.2%, P < 0.01); and the specificity of the patients with the duration of illness < 1 year was 94.2%, not significantly different from that of the patients with the duration of illness > 1 year (95.2%, P = 0.94). CONCLUSION: With relatively high sensitivity and specificity, anti-CCP antibody may be a useful parameter in the clinical diagnosis pf RA.