Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

María C. Ávila-Arcos; Marcela Sandoval-Velasco; Hannes Schroeder; Meredith L. Carpenter; Anna-Sapfo Malaspinas; Nathan Wales; Fernando Peñaloza; Carlos D Bustamante; M. Thomas P. Gilbert

doi:10.1111/2041-210X.12353

Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

María C. Ávila-Arcos^*, Marcela Sandoval-Velasco, Hannes Schroeder, Meredith L. Carpenter, Anna-Sapfo Malaspinas, Nathan Wales, Fernando Peñaloza, Carlos D Bustamante, M. Thomas P. Gilbert

^*Corresponding author for this work

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Abstract

Application of whole-genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing. We compared the performance of two recent WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded and single-stranded build protocols. Although both methods effectively enriched aDNA, we observed consistent differences between the methods, providing the opportunity to further explore parameters influencing WGC experiments. Our results suggest bait length has a potential influence on library enrichment. Moreover, we show WGC biases against shorter molecules that are enriched in single-stranded libraries preparation protocols. Lastly, we document the effect of WGC on features including clonality, GC composition and repetitive DNA content. Our findings provide insights relevant to those planning WGC on aDNA and suggest future tests and optimization to improve WGC efficiency. Copyright

Original language	English
Pages (from-to)	725-734
Number of pages	10
Journal	Methods in ecology and evolution
Volume	6
Issue number	6
DOIs	https://doi.org/10.1111/2041-210X.12353
Publication status	Published - 1 Jun 2015

Keywords

Ancient DNA
Bioinformatics
Genomes
Laboratory methods
Molecular biology
Sequence data

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10.1111/2041-210X.12353

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abstract = "Application of whole-genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing. We compared the performance of two recent WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded and single-stranded build protocols. Although both methods effectively enriched aDNA, we observed consistent differences between the methods, providing the opportunity to further explore parameters influencing WGC experiments. Our results suggest bait length has a potential influence on library enrichment. Moreover, we show WGC biases against shorter molecules that are enriched in single-stranded libraries preparation protocols. Lastly, we document the effect of WGC on features including clonality, GC composition and repetitive DNA content. Our findings provide insights relevant to those planning WGC on aDNA and suggest future tests and optimization to improve WGC efficiency. Copyright",

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AU - Ávila-Arcos, María C.

AU - Sandoval-Velasco, Marcela

AU - Schroeder, Hannes

AU - Carpenter, Meredith L.

AU - Malaspinas, Anna-Sapfo

AU - Wales, Nathan

AU - Peñaloza, Fernando

AU - Bustamante, Carlos D

AU - Gilbert, M. Thomas P.

PY - 2015/6/1

Y1 - 2015/6/1

N2 - Application of whole-genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing. We compared the performance of two recent WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded and single-stranded build protocols. Although both methods effectively enriched aDNA, we observed consistent differences between the methods, providing the opportunity to further explore parameters influencing WGC experiments. Our results suggest bait length has a potential influence on library enrichment. Moreover, we show WGC biases against shorter molecules that are enriched in single-stranded libraries preparation protocols. Lastly, we document the effect of WGC on features including clonality, GC composition and repetitive DNA content. Our findings provide insights relevant to those planning WGC on aDNA and suggest future tests and optimization to improve WGC efficiency. Copyright

AB - Application of whole-genome capture (WGC) methods to ancient DNA (aDNA) promises to increase efficiency of ancient genome sequencing. We compared the performance of two recent WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded and single-stranded build protocols. Although both methods effectively enriched aDNA, we observed consistent differences between the methods, providing the opportunity to further explore parameters influencing WGC experiments. Our results suggest bait length has a potential influence on library enrichment. Moreover, we show WGC biases against shorter molecules that are enriched in single-stranded libraries preparation protocols. Lastly, we document the effect of WGC on features including clonality, GC composition and repetitive DNA content. Our findings provide insights relevant to those planning WGC on aDNA and suggest future tests and optimization to improve WGC efficiency. Copyright

KW - Ancient DNA

KW - Bioinformatics

KW - Genomes

KW - Laboratory methods

KW - Molecular biology

KW - Sequence data

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Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

Abstract

Keywords

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