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Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

ABSTRACT: Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

PROVIDER: PRJEB27504 | ENA |

REPOSITORIES: ENA

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Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform.

Project description:BackgroundMassively-parallel-sequencing, coupled with sample multiplexing, has made genetic tests broadly affordable. However, intractable index mis-assignments (commonly exceeds 1%) were repeatedly reported on some widely used sequencing platforms.ResultsHere, we investigated this quality issue on BGI sequencers using three library preparation methods: whole genome sequencing (WGS) with PCR, PCR-free WGS, and two-step targeted PCR. BGI's sequencers utilize a unique DNA nanoball (DNB) technology which uses rolling circle replication for DNA-nanoball preparation; this linear amplification is PCR free and can avoid error accumulation. We demonstrated that single index mis-assignment from free indexed oligos occurs at a rate of one in 36 million reads, suggesting virtually no index hopping during DNB creation and arraying. Furthermore, the DNB-based NGS libraries have achieved an unprecedentedly low sample-to-sample mis-assignment rate of 0.0001 to 0.0004% under recommended procedures.ConclusionsSingle indexing with DNB technology provides a simple but effective method for sensitive genetic assays with large sample numbers.

| S-EPMC6416933 | biostudies-literature

DNA-seq of Candida albians strains engineered with increasing levels of leucine mis-incorporation at CUG codon, SYBARIS project

Project description:The aim of this experiment is to test how atypical codon assignment (in our case Ser and Leu at CUG sites) flexibility can provide an effective mechanism to alter the genetic code. We have reengineered C. albicans strains to mis-incorporate increasing levels of Leu at protein CUG sites.

2016-04-30 | E-SYBR-7 | biostudies-arrayexpress

Benchmarking dataset for measurement and removal of index hopping artifacts in multiplexed droplet-based single-cell RNA-seq data

Project description:Sample index hopping refers to the incorrect sample assignment of a demultiplexed sequencing read in a library pool. To enable benchmarking of methods for measurement of index hopping rate and removal of its artifacts in single-cell RNA-seq data, we developed a validation dataset consisting of a multiplexed library of two samples, in which the true sample of origin of most reads are known. The reads with known sample of origin provide the ground truth for measuring the performance of index hopping correcting methods.

2020-05-09 | GSE149087 | GEO

Body mass index alone may not serve as a reliable indicator of the risk of developing rheumatoid arthritis

Project description:Body mass index alone may not serve as a reliable indicator of the risk of developing rheumatoid arthritis

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Panicum virgatum strain:MIS | cultivar:MIS

Project description:Panicum virgatum MIS Resequencing genome sequencing

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Effect of myocardin mis-expression in human skeletal myoblasts

Project description:transcriptional effects of mis-expression of full length (935) myocardin in growing human skeletal myoblasts Keywords: mis-expression of transcriptional co-activator

2005-10-27 | GSE3378 | GEO

Multisystem inflammatory syndrome in children (MIS-C) serum proteomics

Project description:While fewer cases of severe Coronavirus Disease 2019 (COVID-19) are reported globally in children, a small proportion of SARS-CoV-2 infected children develop a novel pediatric febrile entity called multisystem inflammatory syndrome in children (MIS-C) that develops 2 to 5 weeks after initial SARS-CoV-2 exposure. MIS-C primarily effects male children and children of Hispanic or black descent. MIS-C manifests as a severe and uncontrolled inflammatory response with multiorgan involvement. A hyperinflammatory state is evidenced by clinical makers of inflammation including high levels of C-reactive protein (CRP), ferritin, and D-dimers, and an increased expression of pro-inflammatory cytokines. Children often present with persistent fever, severe gastrointestinal symptoms, cardiovascular manifestations, respiratory symptoms and neurological symptoms6-11,13. Cardiovascular manifestations include hypotension, shock, cardiac dysfunction, myocarditis and pericardial effusion. In the united states, admission to the intensive care unit occurs in approximately 58% of cases. To understand disease pathogenesis of MIS-C and proteins associated with the severe form of disease we performed proteomics analysis of serum or plasma samples. We collected serum from healthy children (SARS-CoV-2 negative, n=20), mild MIS-C (non-ICU, n=5) and severe MIS-C (ICU, n = 20) patients. MIS-C definition and diagnosis was performed according to CDC guidelines. Healthy adult serum (n = 4) was also used for reference ranges quality control and we obtained plasma samples from Kawasaki Disease (KD; n=7) patients that were recruited before the Coronavirus Disease 2019 (COVID-19) pandemic.

2021-09-29 | PXD025462 | Pride

Computational assignment of cell-cycle stage from single-cell transcriptome data

Project description:In this study, we develop computational tools for assignment of cell-cycle stages from single cell and bulk transcriptome data. We perform bulk RNA-Sequencing for mouse embryonic stem cells with known cell cycle stage.

2015-12-01 | E-MTAB-3749 | biostudies-arrayexpress

Mitochondrial diversity study of Xiphinema index

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Assignment of unknown contigs to chicken microchromosome 16 (GGA16)

Project description:Trisomy mapping has long been a powerful means for assigning genes to chicken microchromosome 16 (GGA16). The major histocompatibility complex (MHC-Y, MHC-B) and CD1 genes were previously assigned to GGA16 by trisomy mapping. Here we combined array comparative genomic hybridization (aCGH) with trisomy mapping to investigate unassigned genomic contigs (temporarily assigned to chrUn_random) by the chicken genome sequencing projects for sequences originating from GGA16. We used the Cornell Trisomy chicken line in our study, as this line contains an extra copy of GGA16 and crosses between these individuals generate disomic, trisomic, and tetrasomic GGA16 offspring. Through the analysis of these individuals with aCGH, we compare signal intensities from unknowns to those expected based on copy number, and putatively assign or reject assignment to GGA16 accordingly.

2013-11-22 | GSE47690 | GEO

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