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Method: Density separation of petrous bone powders for optimized ancient DNA yields
- Daniel M. Fernandes,
- Kendra A. Sirak,
- Olivia Cheronet,
- Mario Novak,
- Florian Brück,
- Evelyn Zelger,
- Alejandro Llanos-Lizcano,
- Anna Wagner,
- Anna Zettl,
- Kirsten Mandl,
- Kellie Sara Duffet Carlson,
- Victoria Oberreiter,
- Kadir T. Özdoğan,
- Susanna Sawyer,
- Francesco La Pastina,
- Emanuela Borgia,
- Alfredo Coppa,
- Miroslav Dobeš,
- Petr Velemínský,
- David Reich,
- Lynne S. Bell,
- and Ron Pinhasi
Genome Res. April 2023 33: 622-631; Published in Advance April 18, 2023, doi:10.1101/gr.277714.123
...prehistory. Nat Commun 5: 5257. doi:10.1038/ncomms6257 ↵Gansauge M-T, Meyer M. 2013. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8: 737–748. doi:10.1038/nprot.2013.038 ↵Gansauge M-T, Meyer M. 2019. A method for single-stranded ancient DNA library...
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Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
- Nadin Rohland,
- Swapan Mallick,
- Matthew Mah,
- Robert Maier,
- Nick Patterson,
- and David Reich
Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
...oligonucleotides that are free in solution as baits to fish out complementary sequences in a DNA library (Gnirke et al. 2009) has been transformative for studying ancient DNA. Under appropriate chemical and temperature conditions, these baits hybridize to targeted molecules so other molecules can be washed away...
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Method: A minimally destructive protocol for DNA extraction from ancient teeth
- Éadaoin Harney,
- Olivia Cheronet,
- Daniel M. Fernandes,
- Kendra Sirak,
- Matthew Mah,
- Rebecca Bernardos,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Ann Marie Lawson,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Francesca Candilio,
- Mihai Constantinescu,
- Alfredo Coppa,
- Ion Ciobanu,
- János Dani,
- Zsolt Gallina,
- Francesco Genchi,
- Emese Gyöngyvér Nagy,
- Tamás Hajdu,
- Magdolna Hellebrandt,
- Antónia Horváth,
- Ágnes Király,
- Krisztián Kiss,
- Barbara Kolozsi,
- Péter Kovács,
- Kitti Köhler,
- Michaela Lucci,
- Ildikó Pap,
- Sergiu Popovici,
- Pál Raczky,
- Angela Simalcsik,
- Tamás Szeniczey,
- Sergey Vasilyev,
- Cristian Virag,
- Nadin Rohland,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2021 31: 472-483; Published in Advance February 12, 2021, doi:10.1101/gr.267534.120
...extract using UDG-treatment methods, as described in Rohland et al. (2015) and Gansauge et al. (2020), respectively. These methods remove ancient DNA damage at the interior of each DNA sequence, while preserving characteristic ancient DNA damage at the terminal ends of the molecules, to be used...
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Method: Human auditory ossicles as an alternative optimal source of ancient DNA
- Kendra Sirak,
- Daniel Fernandes,
- Olivia Cheronet,
- Eadaoin Harney,
- Matthew Mah,
- Swapan Mallick,
- Nadin Rohland,
- Nicole Adamski,
- Nasreen Broomandkhoshbacht,
- Kimberly Callan,
- Francesca Candilio,
- Ann Marie Lawson,
- Kirsten Mandl,
- Jonas Oppenheimer,
- Kristin Stewardson,
- Fatma Zalzala,
- Alexandra Anders,
- Juraj Bartík,
- Alfredo Coppa,
- Tumen Dashtseveg,
- Sándor Évinger,
- Zdeněk Farkaš,
- Tamás Hajdu,
- Jamsranjav Bayarsaikhan,
- Lauren McIntyre,
- Vyacheslav Moiseyev,
- Mercedes Okumura,
- Ildikó Pap,
- Michael Pietrusewsky,
- Pál Raczky,
- Alena Šefčáková,
- Andrei Soficaru,
- Tamás Szeniczey,
- Béla Miklós Szőke,
- Dennis Van Gerven,
- Sergey Vasilyev,
- Lynne Bell,
- David Reich,
- and Ron Pinhasi
Genome Res. March 2020 30: 427-436; Published in Advance February 25, 2020, doi:10.1101/gr.260141.119
...DNA recovered and frequency of damage at the terminal nucleotide of the DNA molecule (a commonly used measure of ancient DNA authenticity). Based on these results, we selected an additional 16 archaeological samples for further study from a wide range of geographic locations with varying climates...
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Method: Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples
- Lukas Bokelmann,
- Isabelle Glocke,
- and Matthias Meyer
Genome Res. October 2020 30: 1449-1457; Published in Advance September 22, 2020, doi:10.1101/gr.263863.120
...apoptosis in the trophoblast surrounding the fetus (Tjoa et al. 2006).Beyond the identification of genetic variants, the sequencing of billions of DNA fragments has allowed inferences about the structures of molecules and characteristics of DNA damage that have proven critical for the development of new...
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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
...and methylation information cannot be directly obtained from short-read sequencing because amplification of the original DNA molecule is necessary for clustering. We and others have therefore used the redundancy of the double-stranded DNA to identify DNA methylation information and genomic variants simultaneously...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...is a bias against >5-kbp-long transcripts, probably owing to incomplete reverse transcription. To overcome this limitation, size-selection of cDNAs before sequencing could be a potential solution. This has been successfully shown to sequence a 106-kbp-long transcript from the mouse Ttn gene (Uapinyoying et...
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Method: Extending the spectrum of DNA sequences retrieved from ancient bones and teeth
- Isabelle Glocke and
- Matthias Meyer
Genome Res. July 2017 27: 1230-1237; Published in Advance April 13, 2017, doi:10.1101/gr.219675.116
...in library preparation. The efficiency of library preparation is determined by comparing the number of oligonucleotide library molecules generated in the sample libraries to those in extraction and library blanks. Sequencing the shortest ancient DNA fragments Genome Research 1233 www..org preserved...
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Method: Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS)
- Daniela Nachmanson,
- Shenyi Lian,
- Elizabeth K. Schmidt,
- Michael J. Hipp,
- Kathryn T. Baker,
- Yuezheng Zhang,
- Maria Tretiakova,
- Kaitlyn Loubet-Senear,
- Brendan F. Kohrn,
- Jesse J. Salk,
- Scott R. Kennedy,
- and Rosa Ana Risques
Genome Res. October 2018 28: 1589-1599; Published in Advance September 19, 2018, doi:10.1101/gr.235291.118
...represents the anti-reference strand. (B) Size selection using 0.5× SPRI beads. Uncut, genomic DNA binds to the beads and allows the recovery of the homogenously sized excised fragments in solution. (C) Double-stranded DNA molecule fragmented and ligated with double-stranded DS adapters. Adapters contain 10...
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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
...sequencing depth. The percentage of IESs involved in at least one IES–IES junction is indicated above the barplot.Genome-wide detection of transient IES–IES junctionsWe took advantage of the purity of FANS-sorted anlagen to increase our ability to detect transient DNA molecules produced during IES excision...

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