Cost-effective straightforward method for captured whole
mitogenome sequencing of ancient DNA

J 2021

Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA

ŠENOVSKÁ, Anna, Eva DROZDOVÁ, Ondřej VACULÍK, Filip PARDY, Kristýna BRZOBOHATÁ et. al.

Základní údaje

Originální název

Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA

Autoři

ŠENOVSKÁ, Anna (203 Česká republika, garant, domácí), Eva DROZDOVÁ (203 Česká republika, domácí), Ondřej VACULÍK (203 Česká republika, domácí), Filip PARDY (203 Česká republika, domácí), Kristýna BRZOBOHATÁ (203 Česká republika, domácí), Dana FIALOVÁ (203 Česká republika, domácí), Jaromír ŠMERDA a Petr KOS

Vydání

Forensic Science International, Clare (Ireland), Elsevier, 2021, 0379-0738

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10603 Genetics and heredity

Stát vydavatele

Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.676

Kód RIV

RIV/00216224:14310/21:00120836

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1016/j.forsciint.2020.110638

UT WoS

000754746700004

Klíčová slova anglicky

Ancient DNA; Mitochondrial DNA; Mitogenome; Capture; Enrichment; Sequencing

Štítky

CF GEN, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 15. 10. 2024 09:28, Ing. Martina Blahová

Anotace

V originále

Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.

Návaznosti

MUNI/A/0958/2018, interní kód MU

Název: Podpora výzkumné činnosti studentů molekulární biologie a genetiky 7 (Akronym: MBG 7)

Investor: Masarykova univerzita, Podpora výzkumné činnosti studentů molekulární biologie a genetiky 7, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

90091, velká výzkumná infrastruktura

Název: NCMG

Citovat

ŠENOVSKÁ, Anna, Eva DROZDOVÁ, Ondřej VACULÍK, Filip PARDY, Kristýna BRZOBOHATÁ, Dana FIALOVÁ, Jaromír ŠMERDA a Petr KOS. Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA. Forensic Science International. Clare (Ireland): Elsevier, 2021, roč. 319, February 2021, s. 1-7. ISSN 0379-0738. Dostupné z: https://dx.doi.org/10.1016/j.forsciint.2020.110638.

@article{1702916,
   author = {Šenovská, Anna and Drozdová, Eva and Vaculík, Ondřej and Pardy, Filip and Brzobohatá, Kristýna and Fialová, Dana and Šmerda, Jaromír and Kos, Petr},
   article_location = {Clare (Ireland)},
   article_number = {February 2021},
   doi = {http://dx.doi.org/10.1016/j.forsciint.2020.110638},
   keywords = {Ancient DNA; Mitochondrial DNA; Mitogenome; Capture; Enrichment; Sequencing},
   language = {eng},
   issn = {0379-0738},
   journal = {Forensic Science International},
   title = {Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA},
   url = {https://doi.org/10.1016/j.forsciint.2020.110638},
   volume = {319},
   year = {2021}
}

TY  - JOUR
ID  - 1702916
AU  - Šenovská, Anna - Drozdová, Eva - Vaculík, Ondřej - Pardy, Filip - Brzobohatá, Kristýna - Fialová, Dana - Šmerda, Jaromír - Kos, Petr
PY  - 2021
TI  - Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA
JF  - Forensic Science International
VL  - 319
IS  - February 2021
SP  - 1-7
EP  - 1-7
PB  - Elsevier
SN  - 03790738
KW  - Ancient DNA
KW  - Mitochondrial DNA
KW  - Mitogenome
KW  - Capture
KW  - Enrichment
KW  - Sequencing
UR  - https://doi.org/10.1016/j.forsciint.2020.110638
L2  - https://doi.org/10.1016/j.forsciint.2020.110638
N2  - Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.
ER  -

ŠENOVSKÁ, Anna, Eva DROZDOVÁ, Ondřej VACULÍK, Filip PARDY, Kristýna BRZOBOHATÁ, Dana FIALOVÁ, Jaromír ŠMERDA a Petr KOS. Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA. \textit{Forensic Science International}. Clare (Ireland): Elsevier, 2021, roč.~319, February 2021, s.~1-7. ISSN~0379-0738. Dostupné z: https://dx.doi.org/10.1016/j.forsciint.2020.110638.

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