title: Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries.
abstract: Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Meredith L
authors.initials: ML
authors.lastname: Carpenter
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Jason D
authors.initials: JD
authors.lastname: Buenrostro
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark; Department of Archaeology, Environment, and Community Planning, Faculty of Humanities and Social Sciences, La Trobe University, Melbourne, VIC 3086, Australia.
authors.forename: Cristina
authors.initials: C
authors.lastname: Valdiosera
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark.
authors.forename: Hannes
authors.initials: H
authors.lastname: Schroeder
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark.
authors.forename: Morten E
authors.initials: ME
authors.lastname: Allentoft
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Martin
authors.initials: M
authors.lastname: Sikora
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark.
authors.forename: Morten
authors.initials: M
authors.lastname: Rasmussen
authors.affiliation: Department of Human Genetics and Génome Québec Innovation Centre, McGill University, Montréal, QC H3A 0G1, Canada.
authors.forename: Simon
authors.initials: S
authors.lastname: Gravel
authors.affiliation: Centro Mallqui, Calle Ugarte y Moscoso 165, San Isidro, Lima 27, Peru.
authors.forename: Sonia
authors.initials: S
authors.lastname: Guillén
authors.affiliation: Bulgarian Academy of Sciences, National Institute of Archaeology, Sofia 1000, Bulgaria.
authors.forename: Georgi
authors.initials: G
authors.lastname: Nekhrizov
authors.affiliation: Department of Archaeology, Sofia University St. Kliment Ohridski, Sofia 1504, Bulgaria.
authors.forename: Krasimir
authors.initials: K
authors.lastname: Leshtakov
authors.affiliation: Bulgarian Academy of Sciences, National Institute of Archaeology, Sofia 1000, Bulgaria.
authors.forename: Diana
authors.initials: D
authors.lastname: Dimitrova
authors.affiliation: Department of Archaeology, Sofia University St. Kliment Ohridski, Sofia 1504, Bulgaria.
authors.forename: Nikola
authors.initials: N
authors.lastname: Theodossiev
authors.affiliation: Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Pettener
authors.affiliation: Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126 Bologna, Italy.
authors.forename: Donata
authors.initials: D
authors.lastname: Luiselli
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Karla
authors.initials: K
authors.lastname: Sandoval
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Andrés
authors.initials: A
authors.lastname: Moreno-Estrada
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China; King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark; Macau University of Science and Technology, Taipa, Macau 999078, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark; Ancient DNA Laboratory, Murdoch University, South Street, Perth, WA 6150, Australia.
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen 1350, Denmark.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: wjg@stanford.edu.
authors.forename: William J
authors.initials: WJ
authors.lastname: Greenleaf
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: cdbustam@stanford.edu.
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
mesh_terms: D000293:Adolescent; D001842:Bone and Bones; D002648:Child; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D005580:Fossils; D015723:Gene Library; D023281:Genomics; D006197:Hair; D059014:High-Throughput Nucleotide Sequencing; D049690:History, Ancient; D006801:Humans; D008297:Male; D009106:Mummies; D009693:Nucleic Acid Hybridization; D025341:Principal Component Analysis; D012313:RNA / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D014070:Tooth
chemical_list: D012313:RNA; D004247:DNA