Dataset Information

PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes.

ABSTRACT: Thousands of genomic structural variants (SVs) segregate in the human population and can impact phenotypic traits and diseases. Their identification in whole-genome sequence data of large cohorts is a major computational challenge. Most current approaches identify SVs in single genomes and afterwards merge the identified variants into a joint call set across many genomes. We describe the approach PopDel, which directly identifies deletions of about 500 to at least 10,000?bp in length in data of many genomes jointly, eliminating the need for subsequent variant merging. PopDel scales to tens of thousands of genomes as we demonstrate in evaluations on up to 49,962 genomes. We show that PopDel reliably reports common, rare and de novo deletions. On genomes with available high-confidence reference call sets PopDel shows excellent recall and precision. Genotype inheritance patterns in up to 6794 trios indicate that genotypes predicted by PopDel are more reliable than those of previous SV callers. Furthermore, PopDel's running time is competitive with the fastest tested previous tools. The demonstrated scalability and accuracy of PopDel enables routine scans for deletions in large-scale sequencing studies.

SUBMITTER: Niehus S

PROVIDER: S-EPMC7851401 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes.

Niehus Sebastian S Jónsson Hákon H Schönberger Janina J Björnsson Eythór E Beyter Doruk D Eggertsson Hannes P HP Sulem Patrick P Stefánsson Kári K Halldórsson Bjarni V BV Kehr Birte B

Nature communications 20210201 1

Thousands of genomic structural variants (SVs) segregate in the human population and can impact phenotypic traits and diseases. Their identification in whole-genome sequence data of large cohorts is a major computational challenge. Most current approaches identify SVs in single genomes and afterwards merge the identified variants into a joint call set across many genomes. We describe the approach PopDel, which directly identifies deletions of about 500 to at least 10,000 bp in length in data of ...[more]

PMID: 33526789

Similar Datasets

Project description:While mechanical abrasion by water and sediment is a primary and critical step in weathering process, the upsurge of discarded face masks will undoubtedly become a potential source of micro-/nanofibers owing to the spread of novel coronavirus (COVID-19) pneumonia. However, effects of mechanical abrasion on discarded face masks have neither been seriously addressed nor understood. Therefore, we conducted a simulated experiment to explore abundance, size distribution and morphology of microfibers released from common, surgical and face filtering piece (FFP) masks after mechanical abrasion. Technologies such as Fourier transform infrared spectrometry, fluorescence microscopy, scanning electron microscopy, and confocal laser scanning microscopy were used. Results showed that the abundance of released microfibers followed order of surgical > common > FFP in both water and sediment environments, and the maximum abundance reached 272 ± 12.49 items per square centimeter of mask (items·cm-2) after sediment abrasion. Taking surgical mask for further investigation, the length of released fiber was observed to vary from 47.78 μm to 3.93 mm, and 72.41-89.58% of the total number of released microfibers fell in the range of 0.1-1 mm. However, microfibers with a very small length (1-100 μm) can occupy 0.09-13.59% of the total number of released fibers in sediment environment. The roughness of fiber surface after sediment abrasion was successively increased. Furthermore, the morphology analysis showed significant changes with countless cracks and many prominent protrusions on fiber surface after sediment abrasion. The cracks and protrusions may further accelerate mask decomposition, thereby potentially resulting in the adsorption of other contaminants and the release of self-containing chemicals. This study provides a valuable database of microfibers released from discarded face masks at the primary but critical stage, and further contributes knowledge on environmental impact of discarded personal protective equipment due to COVID-19.

Dataset Information

PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes.

Publications

PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets