Evidence map›Paper›PMID 29739332›Full record

ArticleBMC genomics2018

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.

Maura Costello, Mark Fleharty, Justin Abreu, Yossi Farjoun, Steven Ferriera, Laurie Holmes, Brian Granger, Lisa Green, Tom Howd, Tamara Mason and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
131citing papers in PubMed, 1 pooled it
–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

131 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  4. Review
  5. Article
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  7. Article
  8. Article
  9. Review
  10. Article
  11. Review
  12. Article
  13. Practical RNA-Seq with Spike-Ins: A Bench-to-Bioinformatics Guide.Methods in molecular biology (Clifton, N.J.) · 2026
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  14. Comprehensive virome analysis ofFrontiers in insect science · 2026
    Article
  15. Article
  16. Article
  17. Satellite DNA Genomics: The Ongoing Story.International journal of molecular sciences · 2025
    Review
  18. Review
  19. Article
  20. Article

71 more citing papers are in PubMed but not listed here.

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

17 authors.

Maura CostelloBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA. costello@broadinstitute.org.ORCID http://orcid.org/0000-0002-0281-3035
Mark FlehartyBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Justin AbreuBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Yossi FarjounBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Steven FerrieraBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Laurie HolmesBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Brian GrangerBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Lisa GreenBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Tom HowdBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Tamara MasonBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Gina VicenteBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Michael DasilvaBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Wendy BrodeurBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Timothy DeSmetBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Sheila DodgeBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Niall J LennonBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.
Stacey GabrielBroad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA.

Funding

Center for Common Disease GeneticsUM1HG008895 · NHGRI · BROAD INSTITUTE, INC. · PI DALY, MARK JOSEPH, GABRIEL, STACEY · 2016 to 2020
$111.2M
Center for Common Disease UM1HG008895NHGRI NIH HHS UM1 HG008895
6 · The paper itself

Abstract

backgroundHere we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps.

resultsLeveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different library methods can have vastly different swapping rates and that even non-ExAmp chemistry instruments display trace levels of index swapping. We provide methods for eliminating sample data cross contamination by utilizing non-redundant dual indexing for complete filtering of index swapped reads, and share the sequences for 96 non-combinatorial dual indexes we have validated across various library preparation methods and sequencer models. Finally, using computational methods we provide a greater insight into the mechanism of index swapping.

conclusionsIndex swapping in pooled libraries is a prevalent phenomenon that we observe at a rate of 0.2 to 6% in all sequencing runs on HiSeqX, HiSeq 4000/3000, and NovaSeq. Utilizing non-redundant dual indexing allows for the removal (flagging/filtering) of these swapped reads and eliminates swapping induced sample contamination, which is critical for sensitive applications such as RNA-seq, single cell, blood biopsy using circulating tumor DNA, or clinical sequencing.

Indexed as

High-Throughput Nucleotide SequencingDNAGene LibraryGenome, HumanHumansSequence AnalysisSequence Analysis, DNADNABarcodesExclusion amplificationILLUMINA sequencingIndexIndexesIndex hoppingIndex swappingMassively parallel sequencingMultiplexingNext generation sequencing

Identifiers

PMID29739332
PMCPMC5941783

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.