Dietary composition and feeding strategy of Leptodactylus fuscus (Anura: Leptodactylidae) from a suburban area of the Caribbean Region of Colombia

The use of trophic resources by anurans may be influenced by sexual dimorphism, ontogenetic variation and resources available in the environment. However, most studies on anuran feeding behavior lack of environmental prey availability data. In this study, the dietary composition and the feeding strategy of Leptodactylus fuscus were evaluated considering the availability of potential prey in a sub-urban area of the Colombian Caribbean Region. Additionally, differences in diet composition between adult and juvenile’ frogs were assessed. Prey items were obtained through forced regurgitation technique and prey availability was assessed using pitfall traps. The importance of each prey category and prey selectivity were evaluated through a relative importance index and a food selection index, respectively. Twenty-four stomachs were analyzed, being Hymenoptera the most important prey category and the most abundant resource in the environment. The population of L. fuscus showed a low prey selectivity and prey size was associated with frog’s body size. However, there was no variation in numeric and volumetric dietary composition related to ontogeny. Considering the relationship between the diet and prey availability, our results evidenced L. fuscus exhibits a generalist and opportunistic feeding behavior, which highlight the importance of including information on prey availability to better understand the anurans dietary behavior.Asociación Herpetológica Argentin

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

Background Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. Results We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. Conclusion We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Dietary composition and feeding strategy of Leptodactylus fuscus (Anura: Leptodactylidae) from a suburban area of the Caribbean Region of Colombia

The use of trophic resources by anurans may be influenced by sexual dimorphism, ontogenetic variation and resources available in the environment. However, most studies on anuran feeding behavior lack of environmental prey availability data. In this study, the dietary composition and the feeding strategy of Leptodactylus fuscus were evaluated considering the availability of potential prey in a sub-urban area of the Colombian Caribbean Region. Additionally, differences in diet composition between adult and juvenile’ frogs were assessed. Prey items were obtained through forced regurgitation technique and prey availability was assessed using pitfall traps. The importance of each prey category and prey selectivity were evaluated through a relative importance index and a food selection index, respectively. Twenty-four stomachs were analyzed, being Hymenoptera the most important prey category and the most abundant resource in the environment. The population of L. fuscus showed a low prey selectivity and prey size was associated with frog’s body size. However, there was no variation in numeric and volumetric dietary composition related to ontogeny. Considering the relationship between the diet and prey availability, our results evidenced L. fuscus exhibits a generalist and opportunistic feeding behavior, which highlight the importance of including information on prey availability to better understand the anurans dietary behavior.Asociación Herpetológica Argentin

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose: Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods: Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results: We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion: The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock