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.

Basic information

Original name

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

Authors

ŠENOVSKÁ, Anna (203 Czech Republic, guarantor, belonging to the institution), Eva DROZDOVÁ (203 Czech Republic, belonging to the institution), Ondřej VACULÍK (203 Czech Republic, belonging to the institution), Filip PARDY (203 Czech Republic, belonging to the institution), Kristýna BRZOBOHATÁ (203 Czech Republic, belonging to the institution), Dana FIALOVÁ (203 Czech Republic, belonging to the institution), Jaromír ŠMERDA and Petr KOS

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10603 Genetics and heredity

Country of publisher

Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.676

RIV identification code

RIV/00216224:14310/21:00120836

Organization unit

Faculty of Science

DOI

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

UT WoS

000754746700004

Keywords in English

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

Abstract

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.

Links

MUNI/A/0958/2018, interní kód MU

Name: Podpora výzkumné činnosti studentů molekulární biologie a genetiky 7 (Acronym: MBG 7)

Investor: Masaryk University, Category A

90091, large research infrastructures

Name: NCMG

Citovat

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

Detailed Information on Publication Record