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The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.

ABSTRACT: Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%). High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.

SUBMITTER: Hendriks KP

PROVIDER: S-EPMC8312739 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.

Hendriks Kasper P KP Mandáková Terezie T Hay Nikolai M NM Ly Elfy E Hooft van Huysduynen Alex A Tamrakar Rubin R Thomas Shawn K SK Toro-Núñez Oscar O Pires J Chris JC Nikolov Lachezar A LA Koch Marcus A MA Windham Michael D MD Lysak Martin A MA Forest Félix F Mummenhoff Klaus K Baker William J WJ Lens Frederic F Bailey C Donovan CD

Applications in plant sciences 20210707 7

<h4>Premise</h4>Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort.<h4>Methods and results</h4>Using 26 Brassicaceae libraries and standard enrich ...[more]

PMID: 34336398

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Project description:PurposeTo allow for comprehensive noninvasive diagnostics of coronary artery disease (CAD) by using three-dimensional (3D) image fusion of CT coronary angiography, CT-derived fractional flow reserve (CT FFR), whole-heart dynamic 3D cardiac MRI perfusion, and 3D cardiac MRI late gadolinium enhancement (LGE).Materials and methodsSeventeen patients (54 years ± 10 [standard deviation], one female) who underwent cardiac CT and cardiac MRI were included (combined subcohort of three prospective trials). Software facilitating multimodal 3D image fusion was developed. Postprocessing of CT data included segmentation of the coronary tree and heart contours, calculation of CT FFR values, and color coding of the coronary tree according to CT FFR. Postprocessing of cardiac MRI data included segmentation of the left ventricle (LV) in cardiac MRI perfusion and cardiac MRI LGE, co-registration of cardiac MRI to CT data, and projection of cardiac MRI perfusion and LGE values onto the high spatial resolution LV from CT.ResultsImage quality was rated as good to excellent (scores: 2.5-2.6; 3 = excellent). CT coronary angiography revealed significant stenoses in seven of 17 cases (41%). CT FFR was possible in 16 of 17 cases (94%) and showed pathologic flow in seven of 17 cases (41%), six of which coincided with cases revealing significant stenoses at CT coronary angiography. Cardiac MRI perfusion identified eight of 17 patients (47%) with hypoperfusion (ischemic burden of 17% ± 5). Cardiac MRI LGE showed myocardial scar in three of 17 cases (18%, scar burden of 7% ± 4). Conventional two-dimensional readout of CT coronary angiography and cardiac MRI resulted in eight of 17 cases (47%) with uncertain findings. Most of these divergent findings could be solved when adding information from CT FFR and 3D image fusion (six of eight, 75%).ConclusionMultimodal 3D cardiac image fusion is feasible and may help with comprehensive noninvasive CAD diagnostics.Supplemental material is available for this article.© RSNA, 2020.

Project description:Abstract Biceps tendinopathy and superior labrum anterior posterior lesions are a common source of shoulder pain and disability and can be effectively treated with biceps tenodesis. There are a variety of open and arthroscopic tenodesis techniques, but no one technique has demonstrated superiority. Arthroscopic techniques often disregard the extra-articular portions of the biceps tendon as a potential source of pain. Open techniques address this concern; however, they can be associated with wound complications, increased blood loss, nerve injury, and disruptions to surgical workflow. Here, we describe an all arthroscopic tenodesis technique at the suprapectoral zone of the tendon. This method addresses extra-articular sources of pain, while limiting the potential pitfalls of open surgery. Technique Video Video 1 Narrated technique video. Standard posterior, anterior, lateral, and low anterior portals are used during the technique. Viewing from the posterior portal in a right shoulder the biceps anchor is debrided to a stable base. A BirdBeak device is inserted through the standard anterior portal and pierces the biceps tendon as laterally as possible, and an 18-gauge spinal needle is used to tease the suture from the BirdBeak device. After a standard subacromial decompression is performed the camera is inserted into the standard lateral portal, and an anterior subdeltoid bursectomy is performed to provide adequate visualization of the tenodesis site. An accessory low anterior portal is created about 1.5 cm proximal to the pectoralis major tendon insertion. The pectoralis major insertion site is used to aid in localization of the tendon just proximal to the subdeltoid portion of the tendon. An 11-blade is inserted through the low anterior portal and used to incise the transverse humeral ligament; the biceps tendon will often bulge from beneath the ligament at this step, confirming appropriate position. The bicep tendon is retracted with the probe, and a noncannulated 8-mm reamer is inserted into the low anterior portal and used to produce a unicortical tunnel. The tunnel’s edges are debrided using an arthroscopic shaver and the arthroscopic electrocautery device; the inferior portion of the tunnel must be smooth to prevent fraying of the tendon. The biceps tendon is then tensioned appropriately via tension pulled through the previously placed suture. A fork-tipped interference screw is then introduced through the low anterior portal to introduce the biceps tendon into the tenodesis site. The interference screw is then inserted and left 1 mm proud. The residual proximal bicep tendon is then amputated using an arthroscopic biter and removed through the lateral portal. The finished tenodesis site is probed and inspected, and a standard postoperative protocol is used.

Dataset Information

The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.

Publications

The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions.

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