ArticleScientific reports2016
Next Generation Sequencing of Pooled Samples: Guideline for Variants' Filtering.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 55 papers, 1 of them a synthesis that pooled it.
What it found
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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
55 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A multi-step genomic approach prioritized TBKBP1 gene as relevant for multiple sclerosis susceptibility.Journal of neurology · 2022Pooled it
- Tracing the genetic legacy of Malabari goats through complete mitogenome sequencing: evidence of maritime exchange via the historic spice route.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Population genetic variation characterised through serial independent pool-seq: the Cyprus Genome Project.Scientific reports · 2026Article
- Genomic architecture of insertion-deletion (indel) variants in beetal goats of India.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Elucidating the genetic architecture of migratory timing in a songbird migrant, the great reed warbler, Acrocephalus arundinaceus.Biology open · 2025Article
- Imputef: imputation of polyploid genotype classes and allele frequencies.BMC genomics · 2025Article
- Genome-wide copy number variation regions in indigenous (Bos indicus) cattle breeds of Tamil Nadu, India.Animal bioscience · 2025Article
- Variation for QTL alleles associated with total dissolved solids among crop types in a GWAS of a Beta vulgaris diversity panel.The plant genome · 2025Article
- Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.Foods (Basel, Switzerland) · 2025Article
- Optimizing genomic diversity assessments for conservation of Bromus auleticus (Trinius ex Nees) using individual and pooled sequencing.PloS one · 2025Article
- Article
- Multiplexed amplicon sequencing reveals the heterogeneous spatial distribution of pyrethroid resistance mutations in Aedes albopictus mosquito populations in southern France.Parasites & vectors · 2024Article
- Genome resequencing and genome-wide polymorphisms in mosquito vectors Aedes aegypti and Aedes albopictus from south India.Scientific reports · 2024Article
- Sampling strategies for genotyping common bean (Frontiers in plant science · 2024Article
- Article
- Deep Learning in Population Genetics.Genome biology and evolution · 2023Article
- First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India.Frontiers in microbiology · 2023Article
- Genomic differentiation in Pacific cod using Pool-Seq.Evolutionary applications · 2022Article
- Utility and challenges of using whole-genome resequencing to detect emerging insect and mite resistance in agroecosystems.Evolutionary applications · 2022Review
- High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing.Plant methods · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing large number of individuals, which is often needed for population genetics studies, is still economically challenging despite falling costs of Next Generation Sequencing (NGS). Pool-seq is an alternative cost- and time-effective option in which DNA from several individuals is pooled for sequencing. However, pooling of DNA creates new problems and challenges for accurate variant call and allele frequency (AF) estimation. In particular, sequencing errors confound with the alleles present at low frequency in the pools possibly giving rise to false positive variants. We sequenced 996 individuals in 83 pools (12 individuals/pool) in a targeted re-sequencing experiment. We show that Pool-seq AFs are robust and reliable by comparing them with public variant databases and in-house SNP-genotyping data of individual subjects of pools. Furthermore, we propose a simple filtering guideline for the removal of spurious variants based on the Kolmogorov-Smirnov statistical test. We experimentally validated our filters by comparing Pool-seq to individual sequencing data showing that the filters remove most of the false variants while retaining majority of true variants. The proposed guideline is fairly generic in nature and could be easily applied in other Pool-seq experiments.
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.