Whole-Genome Capture of Ancient DNA Using Homemade Baits

2019 ◽  
pp. 93-105 ◽  
Author(s):  
Gloria González Fortes ◽  
Johanna L. A. Paijmans
Keyword(s):  
Ancient Dna ◽  
Whole Genome

scholarly journals TKGWV2: An ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data

2021 ◽  
Author(s):  
Daniel M Fernandes ◽  
Olivia Cheronet ◽  
Pere Gelabert ◽  
Ron Pinhasi
Keyword(s):  
Ancient Dna ◽  
Simulated Data ◽  
Error Rates ◽  
Whole Genome Shotgun ◽  
Published Data ◽  
Whole Genome ◽  
False Positive Error ◽  
Kinship Analysis ◽  
Methodological Improvement ◽  
Low Coverage

Estimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1 - 1x minimum average genomic coverage per analysed pair of individuals between. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026x average coverage, or around 1.3 million aligned reads per sample - 4 times less data than 0.1x. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012x, or around 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals previously excluded from kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced.

scholarly journals An Efficient Pipeline for Ancient DNA Mapping and Recovery of Endogenous Ancient DNA from Whole-Genome Sequencing Data

Authorea ◽  
2020 ◽  
Author(s):  
Wenhao Xu ◽  
Yu Lin ◽  
Ke Zhao ◽  
Hai Li ◽  
Yin Tian ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Ancient Dna ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Dna Mapping

scholarly journals Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries

2014 ◽  
Author(s):  
Maria Avila-Arcos ◽  
Marcela Sandoval-Velasco ◽  
Hannes Schroeder ◽  
Meredith L Carpenter ◽  
Anna-Sapfo Malaspinas ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Repetitive Dna ◽  
Ancient Dna ◽  
Dna Content ◽  
Important Influence ◽  
Whole Genome ◽  
Comparative Performance ◽  
Gc Composition

1. The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing. 2. We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments. 3. Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries. 4. Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.

scholarly journals TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniel M. Fernandes ◽  
Olivia Cheronet ◽  
Pere Gelabert ◽  
Ron Pinhasi
Keyword(s):  
Ancient Dna ◽  
Average Length ◽  
Simulated Data ◽  
Error Rates ◽  
Whole Genome Shotgun ◽  
Published Data ◽  
Whole Genome ◽  
False Positive Error ◽  
Kinship Analysis ◽  
Low Coverage

AbstractEstimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1–1× minimum average genomic coverage per analysed pair of individuals. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026× average coverage, or around 18,000 SNPs from 1.3 million aligned reads per sample with average length of 62 bp—four times less data than 0.1× coverage at similar read lengths. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012×, or around 4000 SNPs from 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals that had been excluded from prior kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced.

scholarly journals An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole‐genome sequencing data

2020 ◽  
Author(s):  
Wenhao Xu ◽  
Yu Lin ◽  
Keliang Zhao ◽  
Haimeng Li ◽  
Yinping Tian ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Ancient Dna ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Dna Mapping

scholarly journals Comparative performance of two whole‐genome capture methodologies on ancient DNA Illumina libraries

2015 ◽  
Vol 6 (6) ◽  
pp. 725-734 ◽  
Author(s):  
María C. Ávila‐Arcos ◽  
Marcela Sandoval‐Velasco ◽  
Hannes Schroeder ◽  
Meredith L. Carpenter ◽  
Anna‐Sapfo Malaspinas ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Whole Genome ◽  
Comparative Performance

scholarly journals Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

2013 ◽  
Vol 93 (5) ◽  
pp. 852-864 ◽  
Author(s):  
Meredith L. Carpenter ◽  
Jason D. Buenrostro ◽  
Cristina Valdiosera ◽  
Hannes Schroeder ◽  
Morten E. Allentoft ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Ancient Dna ◽  
Whole Genome ◽  
Targeted Enrichment

Whole genome scan identifies several chromosomal regions linked to equine sarcoids

2012 ◽  
Vol 154 (1) ◽  
pp. 19-25 ◽  
Author(s):  
V. Jandova ◽  
J. Klukowska-Rötzler ◽  
G. Dolf ◽  
J. Janda ◽  
P. Roosje ◽  
...  
Keyword(s):  
Genome Scan ◽  
Whole Genome ◽  
Whole Genome Scan

Genetische Untersuchungen während der Schwangerschaft und beim Kind

2013 ◽  
Vol 70 (11) ◽  
pp. 621-631 ◽  
Author(s):  
Deborah Bartholdi ◽  
Peter Miny
Keyword(s):  
Array Cgh ◽  
Neuromuskuläre Erkrankungen ◽  
Whole Genome ◽  
Klinische Diagnostik ◽  
Molekulare Karyotypisierung ◽  
Monogene Erkrankungen ◽  
Genetische Untersuchungen

Neue Schlüsseltechnologien führen gegenwärtig zu einem grundlegenden Wandel im klinischen Einsatz genetischer Labordiagnostik. In der Pränataldiagnostik hat die nicht invasive Abklärung von Aneuploidien im mütterliche Blut Fuß gefasst (NIPT) und dieser Ansatz wird in Zukunft auch bei anderen Chromosomenstörungen und Fragestellungen (monogene Erkrankungen) zum Einsatz kommen. Im postnatalen Bereich hat die Microarray Analyse (Array-CGH, molekulare Karyotypisierung) die konventionelle Chromosomenanalyse bei der Abklärung von Kindern mit Fehlbildungen, einer nicht-syndromalen geistigen Behinderung oder Autismusspektrumstörung abgelöst. Die neuen Hochdurchsatzsequenziermethoden erlauben die effiziente Abklärung von genetisch sehr heterogenen Krankheitsbildern wie z. B. Epilepsien, neuromuskuläre Erkrankungen und Schwerhörigkeit, durch Diagnostik-Panels, bei welchen Dutzende von Genen parallel analysiert werden können. Der Einsatz der Exom oder whole genome Sequenzierung als wissenschaftliche Methode zur Identifizierung von neuen Krankheitsgenen wird auch in der Diagnostik von schweren ungeklärten Erkrankungen oder Entwicklungsstörungen, die genetisch extrem heterogen sind, zum Einsatz kommen. Die neuen Methoden werden die klinische Diagnostik in der Pädiatrie und anderen Bereichen der Medizin über kurz oder lang verändern, indem die genetische Labordiagnostik eher früher im Abklärungsprozess zur Anwendung kommen wird (genetics first).

Ancient DNA

AccessScience ◽  
2015 ◽  
Keyword(s):  
Ancient Dna
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