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

被引：33

作者：

Avila-Arcos, Maria C. ^{[1
,2
]}

Sandoval-Velasco, Marcela ^{[2
]}

Schroeder, Hannes ^{[2
,3
]}

Carpenter, Meredith L. ^{[1
,4
]}

Malaspinas, Anna-Sapfo ^{[2
]}

Wales, Nathan ^{[2
]}

Penaloza, Fernando ^{[2
,4
,5
]}

Bustamante, Carlos D. ^{[1
]}

Gilbert, M. Thomas P. ^{[2
]}

机构：

[1] Stanford Univ, Sch Med, Dept Genet, Stanford, CA 94305 USA

[2] Univ Copenhagen, Ctr GeoGenet, Nat Hist Museum Denmark, DK-1350 Copenhagen K, Denmark

[3] Leiden Univ, Fac Archaeol, NL-2300 Leiden, Netherlands

[4] IdentifyGenomics LLC, Menlo Pk, CA 94025 USA

[5] Univ Nacl Autonoma Mexico, Undergrad Program Genom Sci, Cuernavaca 62210, Morelos, Mexico

来源：

METHODS IN ECOLOGY AND EVOLUTION | 2015年 / 6卷 / 06期

基金：

美国国家科学基金会; 瑞士国家科学基金会;

关键词：

ancient DNA; bioinformatics; genomes; laboratory methods; molecular biology; sequence data; SEQUENCING LIBRARIES; NEANDERTHAL; ENRICHMENT; DAMAGE; CAVE;

D O I：

10.1111/2041-210X.12353

中图分类号：

Q14 [生态学（生物生态学）];

学科分类号：

071012 ; 0713 ;

摘要：

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.

引用

页码：725 / 734

页数：10

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