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发布于:2019-5-30 21:33:41  访问:65 次 回复:0 篇
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HTCP Defined AMD case/control status. SNP: Single nucleotide polymorphism, RAF
Bolded P values are PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23566152 statistically important just after Bonferroni correction (P < 4.5 ?10-3).(RAD51L1), as well as the SNPs for which direct genotyping was not obtained in the additional cases, were not significantly associated with algorithm-identified AMD cases/control status in our study. Recent advances in genotyping and sequencing technology have significantly outpaced the development of HTCP Methyl vanillateProtocol phenotyping capabilities, causing labor-intensive patient identification and DNA collection to be the rate-limiting step in genetic association studies38. As the use of EMR-linked DNA bio-repositories expands, improved HTCP algorithms for cohort selection offers an appealing alternative to automate these processes and share clinically linked genotype data across research fields. These methods are of particular importance for chronic, complex diseases like AMD that are associated with a large number of genetic and environmental risk factors. HTCP algorithms will require a multi-step validation method that achieves sufficiently high phenotyping accuracy, in particular high PPV, necessary for identifying genetic variants that are associated with multifactorial diseases. We found that relying on ICD-9 codes alone for AMD patient selection was not satisfactory. The addition of ICD-9-linked CPT codes or medication records and age restrictions improved algorithm accuracy at identifying both AMD (wet and dry) and control patients. 61 of 11,075 subjects enrolled in the EMR-linked DNA bio-repository were assigned AMD case status by the HTCP algorithm (0.55 ), expectedly lower than the prevalence reported in the age 50 and older population as this database contained subjects of all ages. Demonstrating associations with SNPs previously shown to be associated with AMD, with odds ratios and confidence intervals that substantially overlap with those from the literature, argues that the PPV and NPV achieved by this algorithm are high enough to properly identify AMD cases and controls. The PPV for both dry and wet AMD subtype determination by the algorithm was < 90 (73.3 and 86.7 , respectively) and the FNRs were significantly higher than the FNR for overall AMD case determination (12.0 and 16.1 vs 1.8 ). The relative weakness of the algorithm inScientific RepoRts | 5:12875 | DOi: 10.1038/srepDiscussionwww.nature.com/scientificreports/discriminating AMD subtypes is likely multifactorial and complicated by the spectrum of AMD retinal pathology. Further improvements could include the addition of searchable keywords within the EMR free text in addition to ICD9/CPT codes. Application to a larger AMD cohort will be needed to determine if the algorithm can be reliably used to differentiate wet and dry AMD. Three of the seven previously reported AMD-associated SNPs examined in this study were found to be significantly associated (at Bonferroni correction threshold) with case/control status identified by the HTCP algorithm, and one of the SNPs (rs833069) trended in the opposite direction from that previously PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/20854184 published. Possible explanations for why a lot more SNPs were not significantly connected with case/control status include things like inadequate energy due to sample size or insufficient phenotyping accuracy. Additionally, genetic heterogeneity between the previous populations used to recognize the SNP associations plus the NUGene pr.HTCP Defined AMD case/control status. SNP: Single nucleotide polymorphism, RAF: Risk allele frequency, OR (CI): Odds ratio (95 Confidence Interval).
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