TypeLoader: A fast and efficient automated workflow for the annotation and submission of novel full-length HLA alleles.

Recent years have seen a rapid increase in the discovery of novel allelic variants of the human leukocyte antigen (HLA) genes. Commonly, only the exons encoding the peptide binding domains of novel HLA alleles are submitted. As a result, the IPD-IMGT/HLA Database lacks sequence information outside those regions for the majority of known alleles. This has implications for the application of the new sequencing technologies, which deliver sequence data often covering the complete gene. As these technologies simplify the characterization of the complete gene regions, it is desirable for novel alleles to be submitted as full-length sequences to the database. However, the manual annotation of full-length alleles and the generation of specific formats required by the sequence repositories is prone to error and time consuming. We have developed TypeLoader to address both these facets. With only the full-length sequence as a starting point, Typeloader performs automatic sequence annotation and subsequently handles all steps involved in preparing the specific formats for submission with very little manual intervention. TypeLoader is routinely used at the DKMS Life Science Lab and has aided in the successful submission of more than 900 novel HLA alleles as full-length sequences to the European Nucleotide Archive repository and the IPD-IMGT/HLA Database with a 95% reduction in the time spent on annotation and submission when compared with handling these processes manually. TypeLoader is implemented as a web application and can be easily installed and used on a standalone Linux desktop system or within a Linux client/server architecture. TypeLoader is downloadable from http://www.github.com/DKMS-LSL/typeloader.

Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles.

The high-throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5'- to 3'-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real-time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences. Remaining conflicts are resolved using the R package DR2S (Dual Redundant Reference Sequencing). Given the relatively high throughput of this strategy, we have developed the semi-automated web service TypeLoader, to aid in the submission of sequences to the EMBL-ENA and the IPD-IMGT/HLA Database. In the IPD-IMGT/HLA Database release 3.24.0 (April 2016; prior to the submission of the sequences described here), only 5.2% of all known HLA alleles have been fully characterised together with intronic and UTR sequences. So far, we have applied our strategy to characterise and submit 1056 HLA alleles, thereby more than doubling the number of fully characterised alleles. Given the increasing application of next generation sequencing (NGS) for full gene characterisation in clinical practice, extending the HLA database concomitantly is highly desirable. Therefore, we propose this dual redundant sequencing strategy as a workflow for submission of novel full-length alleles and characterisation of sequences that are as yet incomplete. This would help to mitigate the predominance of partially known alleles in the database.

Is it safe to perform cardiac catheterizations on adults with congenital heart disease in a pediatric catheterization laboratory?

OBJECTIVE: To determine the complication rate during the catheterization in adults with congenital heart disease (CHD) in a pediatric catheterization laboratory (PCL). BACKGROUND: An increasing number of patients with CHD are surviving into adulthood, with diagnostic and interventional cardiac catheterization being essential for the management of their disease. The complication rate during the catheterization of adults with CHD has not been reported. METHODS: A retrospective chart review was performed on all adult patients (>18 years) with CHD who underwent diagnostic or interventional catheterization in our PCL within the past 8.5 years. RESULTS: A total of 576 procedures were performed on 436 adult patients (median age 26 years). Complex heart disease was present in 387/576 (67%) procedures. An isolated atrial septal defect or patent foramen ovale was present in 115/576 (20%) procedures, and 51/576 (9%) procedures were performed on patients with structurally normal hearts with arrhythmias. Interventional catheterization was performed in 378/576 (66%) procedures. There were complications during 61/576 (10.6%) procedures; 19 were considered major and 42 minor. Major complications were death (1), ventricular fibrillation (1), hypotension requiring inotropes (7), atrial flutter (3), retroperitoneal hematoma, pneumothorax, hemothorax, aortic dissection, renal failure, myocardial ischemia and stent malposition (1 each). The most common minor complications were vascular entry site hematomas and hypotension not requiring inotropes. Procedures performed on patients > or = 45 years of age had a 19% occurrence of complications overall compared with 9% occurrence rate in patients of age < 45 years (P < 0.01). CONCLUSIONS: The complication rate during the catheterization of adults with CHD in a PCL is similar to the complication rate of children with CHD undergoing cardiac catheterization. The older subset of patients are more likely to encounter complications overall. The encountered complications could be handled effectively in the PCL. With screening in place, it is safe to perform cardiac catheterization on most adults with CHD in a PCL.

Unusual thickness-dependent heat-capacity anomalies in free-standing hexatic liquid-crystal films.

High-resolution heat-capacity and optical-reflectivity measurements have been conducted near the smectic-A to hexatic-B transition in thin free-standing films of the liquid-crystal compound 64COOBC. We find an unexpected dependence on film thickness of the integrated magnitude of the heat-capacity anomalies as the films undergo layer-by-layer transitions. We measure the penetration depths of the ordering from the surface and next-to-surface layers which are pertinent to the highly correlated thermal behavior.