Evidence map›Paper›PMID 35611117›Full record

ArticleComputational and structural biotechnology journal2022

Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking.

Sara Donzelli, Ludovica Ciuffreda, Martina Pontone, Martina Betti, Alice Massacci, Carla Mottini, Francesca De Nicola, Giulia Orlandi, Frauke Goeman, Eugenia Giuliani and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors.

Sara DonzelliOncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Ludovica CiuffredaSAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Martina PontoneMicrobiology and Virology Unit, IRCCS San Gallicano Dermatological Institute, Rome, Italy.
Martina BettiBiostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Alice MassacciBiostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Carla MottiniSAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Francesca De NicolaSAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Giulia OrlandiScientific Direction, IRCCS San Gallicano Dermatological Institute, Rome, Italy.
Frauke GoemanSAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Eugenia GiulianiScientific Direction, IRCCS San Gallicano Dermatological Institute, Rome, Italy.
Eleonora SperandioBiostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Giulia PiaggioSAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
ISG COVID Team
Aldo MorroneScientific Direction, IRCCS San Gallicano Dermatological Institute, Rome, Italy.
Gennaro CilibertoScientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Maurizio FanciulliSAFU Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Giovanni BlandinoOncogenomics and Epigenetics, IRCCS Regina Elena National Cancer Institute, Rome, Italy.
Fulvia PimpinelliMicrobiology and Virology Unit, IRCCS San Gallicano Dermatological Institute, Rome, Italy.
Matteo PalloccaBiostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The SARS-CoV-2 Variants of Concern tracking via Whole Genome Sequencing represents a pillar of public health measures for the containment of the pandemic. The ability to track down the lineage distribution on a local and global scale leads to a better understanding of immune escape and to adopting interventions to contain novel outbreaks. This scenario poses a challenge for NGS laboratories worldwide that are pressed to have both a faster turnaround time and a high-throughput processing of swabs for sequencing and analysis. In this study, we present an optimization of the Illumina COVID-seq protocol carried out on thousands of SARS-CoV-2 samples at the wet and dry level. We discuss the unique challenges related to processing hundreds of swabs per week such as the tradeoff between ultra-high sensitivity and negative contamination levels, cost efficiency and bioinformatics quality metrics.

Indexed as

BAM, Binary Alignment MapBED, Browser Extensible DataBioinformatics workflowCOVID mutationsFDA, Food and Drug AdministrationHPC, High Performance ComputingIllumina COVID-seqLIMS, Laboratory Information Management SystemNGS, Next Generation SequencingOncologyOncology MetagenomicsRBD, Receptor-Binding DomainSARS-CoV-2 genomeSARS-CoV-2 mutationSARS-CoV-2, Severe Acute Respiratory Syndrome CoronavirusSARS-CoV-2 Variants of ConcernTAT, Turnaround TimeVoC, Variants of Concern

Identifiers

PMID35611117
PMCPMC9119164

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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Registered trials

None linked

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.