Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders

There are >2500 different genetically determined developmental disorders (DD), which, as a group, show very high levels of both locus and allelic heterogeneity. This has led to the wide-spread use of evidence-based filtering of genome-wide sequence data as a diagnostic tool in DD. Determining whether the association of a filtered variant at a specific locus is a plausible explanation of the phenotype in the proband is crucial and commonly requires extensive manual literature review by both clinical scientists and clinicians. Access to a database of weighted clinical features extracted from rigorously curated literature would increase the efficiency of this process and facilitate the development of robust phenotypic similarity metrics. However, given the large and rapidly increasing volume of published information, conventional biocuration approaches are becoming impractical. Here, we present a scalable, automated method for the extraction of categorical phenotypic descriptors from the full-text literature. Papers identified through literature review were downloaded and parsed using the Cadmus custom retrieval package. Human Phenotype Ontology terms were extracted using MetaMap, with 76-84% precision and 65-73% recall. Mean terms per paper increased from 9 in title + abstract, to 68 using full text. We demonstrate that these literature-derived disease models plausibly reflect true disease expressivity more accurately than widely used manually curated models, through comparison with prospectively gathered data from the Deciphering Developmental Disorders study. The area under the curve for receiver operating characteristic (ROC) curves increased by 5-10% through the use of literature-derived models. This work shows that scalable automated literature curation increases performance and adds weight to the need for this strategy to be integrated into informatic variant analysis pipelines. Database URL: https://doi.org/10.1093/database/baac038.

Routine intraoperative laparoscopic cholangiography

BACKGROUND

Whether intraoperative laparoscopic cholangiography should be routine is debatable.

METHODS

We reviewed the cholangiography experience in 669 consecutive laparoscopic cholecystectomies.

RESULTS

Mean age of the patients was 39 years, 78% were female, and 29% had acute cholecystitis. Cholecystectomy was completed laparoscopically in 606 (91%). Laparoscopic cholangiography was completed in 562 (93%) and 348 (62%) were routine (no preoperative indication). The mean operating time in 1996 was 61 minutes. Out of the 348 routine cholangiograms, 17 demonstrated evidence of unsuspected choledocholithiasis. Five patients had choledocholithiasis documented by laparoscopic common bile duct exploration and/or endoscopic retrograde cholangiopancreatography. Two patients had normal postoperative cholangiopancreatography. One of 10 patients managed expectantly was readmitted postoperatively with obstructive jaundice. In 4 patients, routine cholangiography revealed unexpected anatomy, and in 2, this prevented misidentification and transection of the common bile duct.

CONCLUSION

Laparoscopic cholangiography is safe, quick, detects unsuspected choledocholithiasis, and can prevent common bile duct transection. It should be routine.