This page is a stub to be filled in as we conduct research for implementing simulation models of index switching.

Index switching is a particular form of internal contamination (also known as cross contamination) that occurs during sequencing which results in sequence reads being assigned to the incorrect sample during demultiplexing.

There appear to be distinct mechanisms that operate at distinct steps in the measurement workflow but all involving physical movement of index or barcode sequences and result in reads being assigned to an incorrect source sample. Some effort is needed to disambiguate these different processes and the different terminology that has been used (including "tag switching", "index hopping", "index switching").

TODO:

• Synthesize the below references to determine models consistent with the views of these references.
  • Likely these models (for dual-indexing experiments) will be framed in terms of each sample having forward and reverse index sequences and getting misassigned when one or both is swapped and the resulting combination corresponds to another sample (and discarded when the new combination is not valid)
  • Does it make sense to think of switching as occurring between the corresponding indices of two DNA fragments? Or does it involve free index sequences, in which case it depends on the concentrations of free index sequences?
• Consider the role of sample biomass or DNA concentration in determining the dynamics
  • See @hornung2019issu (Section "Index hopping") which suggests that the DNA concentration of a sample is relevant; low-concentration samples can lead to an excess of unligated adapters, which can ligate with DNA fragments from other samples that are not already ligated with an adapter

References

[costello2018char] Costello M, Fleharty M, Abreu J, Farjoun Y, Ferriera S, Holmes L, Granger B, Green L, Howd T, Mason T, Vicente G, Dasilva M, Brodeur W, DeSmet T, Dodge S, Lennon NJ, Gabriel S. 2018. Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms. BMC Genomics 19:332. doi:10.1186/s12864-018-4703-0

[eisenhofer2019cont] Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. 2019. Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol 27:105–117. doi:10.1016/j.tim.2018.11.003

[farouni2020mode] Farouni R, Djambazian H, Ferri LE, Ragoussis J, Najafabadi HS. 2020. Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing. Nat Commun 11:1–8. doi:10.1038/s41467-020-16522-z

[hornung2019issu] Hornung BVH, Zwittink RD, Kuijper EJ. 2019. Issues and current standards of controls in microbiome research. FEMS Microbiol Ecol 95:1–7. doi:10.1093/femsec/fiz045

[illumina2017effe] Illumina. 2017. Effects of Index Misassignment on Multiplexing and Downstream Analysis. https://www.illumina.com/content/dam/illumina-marketing/documents/products/whitepapers/index-hopping-white-paper-770-2017-004.pdf

[larsson2018comp] Larsson AJM, Stanley G, Sinha R, Weissman IL, Sandberg R. 2018. Computational correction of index switching in multiplexed sequencing libraries. Nat Methods 15:305–307. doi:10.1038/nmeth.4666

[li2018reli] Li Q, Zhao X, Zhang W, Wang L, Wang Jingjing, Xu D, Mei Z, Liu Q, Du S, Li Z, Liang X, Wang X, Wei H, Liu P, Zou J, Shen H, Chen A, Drmanac S, Liu JS, Li L, Jiang H, Zhang Y, Wang Jian, Yang H, Xu X, Drmanac R, Jiang Y. 2019. Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform. BMC Genomics 20:215. doi:10.1186/s12864-019-5569-5

[owens2018anov] Owens GL, Todesco M, Drummond EBM, Yeaman S, Rieseberg LH. 2018. A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X. Mol Ecol Resour 18:169–175. doi:10.1111/1755-0998.12713

[schnell2015tagj] Schnell IB, Bohmann K, Gilbert MTP. 2015. Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies. Mol Ecol Resour 15:1289–1303. doi:10.1111/1755-0998.12402

[sinha2017inde] Sinha R, Stanley G, Gulati GS, Ezran C, Travaglini KJ, Wei E, Chan CKF, Nabhan AN, Su T, Morganti RM, Conley SD, Chaib H, Red-Horse K, Longaker MT, Snyder MP, Krasnow MA, Weissman IL. 2017. Index Switching Causes “Spreading-Of-Signal” Among Multiplexed Samples In Illumina HiSeq 4000 DNA Sequencing. bioRxiv 125724. doi:10.1101/125724

[vandervalk2020inde] van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K. 2020. Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies. Mol Ecol Resour 20:1171–1181. doi:10.1111/1755-0998.13009