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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F21%3A00120836" target="_blank" >RIV/00216224:14310/21:00120836 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/48511005:_____/20:N0000024

Výsledek na webu

<a href="https://doi.org/10.1016/j.forsciint.2020.110638" target="_blank" >https://doi.org/10.1016/j.forsciint.2020.110638</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.forsciint.2020.110638" target="_blank" >10.1016/j.forsciint.2020.110638</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10603 - Genetics and heredity (medical genetics to be 3)

Projekt

<a href="/cs/project/LM2015091" target="_blank" >LM2015091: Národní centrum lékařské genomiky</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2021

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Forensic Science International

ISSN

0379-0738

e-ISSN

1872-6283

Svazek periodika

319

Číslo periodika v rámci svazku

February 2021

Stát vydavatele periodika

IE - Irsko

Počet stran výsledku

7

Strana od-do

1-7

Kód UT WoS článku

000754746700004

EID výsledku v databázi Scopus

2-s2.0-85097778404