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Fulltext Pre-operative Assessment of Shoulder Pathologies on MRI by a Radiologist and an Orthopaedic Surgeon

Winkler S, Herbst B, Kafchitsas K, Wohlmuth P, Hoffstetter P, Rueth MJ

Malays Orthop J, 2024 Mar;18(1):42-50.
PMID: 38638663 DOI: 10.5704/MOJ.2403.006

INTRODUCTION: Pathologies of the shoulder, i.e. rotator cuff tears and labral injuries are very common. Most patients receive MRI examination prior to surgery. A correct assessment of pathologies is significant for a detailed patient education and planning of surgery.
MATERIALS AND METHODS: Sixty-nine patients were identified, who underwent both, a standardised shoulder MRI and following arthroscopic shoulder surgery in our hospital. For this retrospective comparative study, the MRIs were pseudonymised and evaluated separately by an orthopaedic surgeon and a radiologist. A third rater evaluated images and reports of shoulder surgery, which served as positive control. Results of all raters were then compared. The aim was an analysis of agreement rates of diagnostic accuracy of preoperative MRI by a radiologist and an orthopaedic surgeon.
RESULTS: The overall agreement with positive control of detecting transmural cuff tears was high (84% and 89%) and lower for partial tears (70-80%). Subscapularis tears were assessed with moderate rates of agreement (60 - 70%) compared to intra-operative findings. Labral pathologies were detected mostly correctly. SLAP lesions and pulley lesions of the LHB were identified with only moderate agreement (66.4% and 57.2%) and had a high inter-rater disagreement.
CONCLUSION: This study demonstrated that tears of the rotator cuff (supraspinatus, infraspinatus) and labral pathologies can be assessed in non-contrast pre-operative shoulder MRI images with a high accuracy. This allows a detailed planning of surgery and aftercare. Pathologies of the subscapularis tendon, SLAP lesions and biceps instabilities are more challenging to detect correctly. There were only small differences between a radiologic and orthopaedic interpretation of the images.
Fulltext Long-read sequencing and genome assembly of natural history collection samples and challenging specimens

Bein B, Chrysostomakis I, Arantes LS, Brown T, Gerheim C, Schell T, et al.

bioRxiv, 2024 Sep 27.
PMID: 39386456 DOI: 10.1101/2024.03.04.583385

Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assembled the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.
Fulltext Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, et al.

Genome Biol, 2021 04 29;22(1):120.
PMID: 33910595 DOI: 10.1186/s13059-021-02336-9

BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.
CONCLUSIONS: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
Fulltext Towards complete and error-free genome assemblies of all vertebrate species

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al.

Nature, 2021 Apr;592(7856):737-746.
PMID: 33911273 DOI: 10.1038/s41586-021-03451-0

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.