Ancestry Publications

van der Valk Tom, T Vezzi, Francesco F et al.

Molecular ecology resourcesMol Ecol ResourIndex hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.117111811171-118110.1111/1755-0998.13009The high-throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low-quantity and low-quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100-year old museum-preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample-specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.© 2019 John Wiley & Sons Ltd.van der ValkTomT0000-0001-6582-3452Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.VezziFrancescoFScience for Life Laboratory, Solna, Sweden.OrmestadMattiasMScience for Life Laboratory, Solna, Sweden.DalénLoveLDepartment of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.GuschanskiKaterinaK0000-0002-8493-5457Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.engJan Löfqvist Endowments of the Royal Physiographic Society of Lund2015-676Svenska Forskningsrådet Formas2016-00835Svenska Forskningsrådet FormasScience for Life LaboratoryKnut and Alice Wallenberg FoundationNational Genomics Infrastructure funded by the Swedish Research CouncilUppsala Multidisciplinary Center for Advanced Computational ScienceJournal Article20190505EnglandMol Ecol Resour1014656041755-098X0DNA, Ancient9007-49-2DNAIMAnimalsDNADNA Barcoding, TaxonomicDNA, AncientGorilla gorillageneticsHigh-Throughput Nucleotide SequencingmethodsSequence Analysis, DNAmethodsancient DNAindex switchingmultiplexingmuseum specimensnext-generation sequencingread misassignment201891020192282019228201939602021876020193960ppublish3084809210.1111/1755-0998.13009REFERENCES

Jatupol Kampuansai, Wibhu Kutanan, Eszter Dudás et al.

Molecular genetics and genomics : MGG

North Sea