ArticleMolecular ecology resources2018
The impact of endogenous content, replicates and pooling on genome capture from faecal samples.
Article in Molecular ecology resources, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Targeted chromosomal sequencing of wild bonobos identifies a genetically distinct subpopulation east of the Lomami river.Genome biology · 2026Article
- Maximizing the Quality of Non-Invasive Samples for Conservation Genetics Using Targeted Next-Generation Sequencing: A Comparison of Fecal DNA Preservation Methodologies.Ecology and evolution · 2026Article
- Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River.bioRxiv : the preprint server for biology · 2026Article
- Scaling-up RADseq methods for large datasets of non-invasive samples: Lessons for library construction and data preprocessing.Molecular ecology resources · 2025Article
- Age Is Just a Number: No Impacts of Scat Ageing on Single Nucleotide Polymorphism Genotyping Using a Target Capture Approach.Ecology and evolution · 2025Article
- Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations.Molecular ecology resources · 2025Article
- Local genetic adaptation to habitat in wild chimpanzees.Science (New York, N.Y.) · 2025Article
- Genome-scale evolution in local populations of wild chimpanzees.Scientific reports · 2025Article
- Local genetic adaptation to habitat in wild chimpanzees.bioRxiv : the preprint server for biology · 2024Article
- Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition.Scientific reports · 2022Article
- Population dynamics and genetic connectivity in recent chimpanzee history.Cell genomics · 2022Article
- Performance and automation of ancient DNA capture with RNA hyRAD probes.Molecular ecology resources · 2022Article
- The genetic impact of an Ebola outbreak on a wild gorilla population.BMC genomics · 2021Article
- HuConTest: Testing Human Contamination in Great Ape Samples.Genome biology and evolution · 2021Article
- The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Urine as a high-quality source of host genomic DNA from wild populations.Molecular ecology resources · 2021Article
- Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement.Computational and structural biotechnology journal · 2021Article
- Genomic targets for high-resolution inference of kinship, ancestry and disease susceptibility in orang-utans (genus: Pongo).BMC genomics · 2020Article
- The impact of endogenous content, replicates and pooling on genome capture from faecal samples.Molecular ecology resources · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.