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Abstract MotivationHaplotagging is a method for linked-read sequencing, which leverages the cost-effectiveness and throughput of short-read sequencing while retaining part of the long-range haplotype information captured by long-read sequencing. Despite its utility and advantages over similar methods, existing linked-read analytical pipelines are incompatible with haplotagging data. ResultsWe describe Harpy, a modular and user-friendly software pipeline for processing all stages of haplotagged linked-read data, from raw sequence data to phased genotypes and structural variant detection. Availability and implementationhttps://github.com/pdimens/harpy. 

Four zebra finches in a closed research colony presented with variable clinical signs, including masses, skin lesions,shivering, and/or ruffled feathers. These birds were not responsive to treatment efforts; 3 died and one was euthanized. All4 were submitted for necropsy to determine the cause of the clinical signs. Gross necropsy and histopathologic findings fromall birds resulted in a diagnosis of round cell neoplasia in multiple organs, including the skin, liver, kidney, and reproductivetract, with intranuclear inclusion bodies in the neoplastic cells. In all 4 cases, immunohistochemical staining showed strongimmunoreactivity for CD3 in 70% to 80% of the neoplastic round cells, with a relatively small subset that were immunopositivefor Pax5. These findings supported a diagnosis of T-cell lymphoma. Frozen liver tissue from one case was submittedfor next-generation sequencing (NGS), which revealed viral RNA with 100% sequence homology to canary polyomavirusstrain 34639 that had originally been identified in a European goldfinch. Formalin-fixed paraffin-embedded scrolls fromanother case were also submitted for NGS, which revealed viral RNA with 97.2% sequence homology to canary polyomavirusstrain 37273 that had originally been identified in a canary. To localize the virus in situ, RNAscope hybridizationwas performed using a probe designed to target the VP1 gene of the sequenced virus in frozen liver tissue. In all 4 cases,disseminated and robust hybridization signals were detected in neoplastic cells. These findings indicate that polyomaviruseshave the potential to be oncogenic in zebra finches.