From cheek swabs to consensus sequences: An A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Andrew C. Clarke, Stefan Prost, Jo Ann L Stanton, W. Timothy J White, Matthew E. Kaplan, Elizabeth A. Matisoo-Smith, Syama Adhikarla, Christina J. Adler, Elena Balanovska, Oleg Balanovsky, Jaume Bertranpetit, David Comas, Alan Cooper, Clio S I Der Sarkissian, Matthew C. Dulik, Jill B. Gaieski, ArunKumar GaneshPrasad, Wolfgang Haak, Marc Haber, Li JinShilin Li, Begoña Martínez-Cruz, Nirav C Merchant, R. John Mitchell, Amanda C. Owings, Laxmi Parida, Ramasamy Pitchappan, Daniel E. Platt, Lluis Quintana-Murci, Colin Renfrew, Daniela R. Lacerda, Ajay K. Royyuru, Fabrício R. Santos, Theodore G. Schurr, Himla Soodyall, Soria Hernanz, Pandikumar Swamikrishnan, Chris Tyler-Smith, Arun Varatharajan Santhakumari, Pedro Paulo Vieira, Miguel G. Vilar, Pierre A. Zalloua, Janet S. Ziegle, R. Spencer Wells

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users.Results: Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling).Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual 'modules' can be swapped out to suit available resources.

Original languageEnglish (US)
Article number68
JournalBMC Genomics
Volume15
Issue number1
DOIs
StatePublished - Jan 25 2014

Fingerprint

High-Throughput Nucleotide Sequencing
Mitochondrial Genome
Cheek
Consensus Sequence
Human Genome
DNA Sequence Analysis
Mitochondrial DNA
DNA
Technology
Polymerase Chain Reaction
Computational Biology
Single Nucleotide Polymorphism
Research Personnel
Genome
Research

Keywords

  • 454 sequencing
  • Bioinformatics
  • Human
  • Long-range PCR
  • Mitochondrial DNA
  • Next-generation sequencing

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Clarke, A. C., Prost, S., Stanton, J. A. L., White, W. T. J., Kaplan, M. E., Matisoo-Smith, E. A., ... Wells, R. S. (2014). From cheek swabs to consensus sequences: An A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics, 15(1), [68]. https://doi.org/10.1186/1471-2164-15-68

From cheek swabs to consensus sequences : An A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. / Clarke, Andrew C.; Prost, Stefan; Stanton, Jo Ann L; White, W. Timothy J; Kaplan, Matthew E.; Matisoo-Smith, Elizabeth A.; Adhikarla, Syama; Adler, Christina J.; Balanovska, Elena; Balanovsky, Oleg; Bertranpetit, Jaume; Comas, David; Cooper, Alan; Der Sarkissian, Clio S I; Dulik, Matthew C.; Gaieski, Jill B.; GaneshPrasad, ArunKumar; Haak, Wolfgang; Haber, Marc; Jin, Li; Li, Shilin; Martínez-Cruz, Begoña; Merchant, Nirav C; Mitchell, R. John; Owings, Amanda C.; Parida, Laxmi; Pitchappan, Ramasamy; Platt, Daniel E.; Quintana-Murci, Lluis; Renfrew, Colin; Lacerda, Daniela R.; Royyuru, Ajay K.; Santos, Fabrício R.; Schurr, Theodore G.; Soodyall, Himla; Hernanz, Soria; Swamikrishnan, Pandikumar; Tyler-Smith, Chris; Santhakumari, Arun Varatharajan; Vieira, Pedro Paulo; Vilar, Miguel G.; Zalloua, Pierre A.; Ziegle, Janet S.; Wells, R. Spencer.

In: BMC Genomics, Vol. 15, No. 1, 68, 25.01.2014.

Research output: Contribution to journalArticle

Clarke, AC, Prost, S, Stanton, JAL, White, WTJ, Kaplan, ME, Matisoo-Smith, EA, Adhikarla, S, Adler, CJ, Balanovska, E, Balanovsky, O, Bertranpetit, J, Comas, D, Cooper, A, Der Sarkissian, CSI, Dulik, MC, Gaieski, JB, GaneshPrasad, A, Haak, W, Haber, M, Jin, L, Li, S, Martínez-Cruz, B, Merchant, NC, Mitchell, RJ, Owings, AC, Parida, L, Pitchappan, R, Platt, DE, Quintana-Murci, L, Renfrew, C, Lacerda, DR, Royyuru, AK, Santos, FR, Schurr, TG, Soodyall, H, Hernanz, S, Swamikrishnan, P, Tyler-Smith, C, Santhakumari, AV, Vieira, PP, Vilar, MG, Zalloua, PA, Ziegle, JS & Wells, RS 2014, 'From cheek swabs to consensus sequences: An A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes', BMC Genomics, vol. 15, no. 1, 68. https://doi.org/10.1186/1471-2164-15-68
Clarke, Andrew C. ; Prost, Stefan ; Stanton, Jo Ann L ; White, W. Timothy J ; Kaplan, Matthew E. ; Matisoo-Smith, Elizabeth A. ; Adhikarla, Syama ; Adler, Christina J. ; Balanovska, Elena ; Balanovsky, Oleg ; Bertranpetit, Jaume ; Comas, David ; Cooper, Alan ; Der Sarkissian, Clio S I ; Dulik, Matthew C. ; Gaieski, Jill B. ; GaneshPrasad, ArunKumar ; Haak, Wolfgang ; Haber, Marc ; Jin, Li ; Li, Shilin ; Martínez-Cruz, Begoña ; Merchant, Nirav C ; Mitchell, R. John ; Owings, Amanda C. ; Parida, Laxmi ; Pitchappan, Ramasamy ; Platt, Daniel E. ; Quintana-Murci, Lluis ; Renfrew, Colin ; Lacerda, Daniela R. ; Royyuru, Ajay K. ; Santos, Fabrício R. ; Schurr, Theodore G. ; Soodyall, Himla ; Hernanz, Soria ; Swamikrishnan, Pandikumar ; Tyler-Smith, Chris ; Santhakumari, Arun Varatharajan ; Vieira, Pedro Paulo ; Vilar, Miguel G. ; Zalloua, Pierre A. ; Ziegle, Janet S. ; Wells, R. Spencer. / From cheek swabs to consensus sequences : An A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. In: BMC Genomics. 2014 ; Vol. 15, No. 1.
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T2 - An A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

AU - Clarke, Andrew C.

AU - Prost, Stefan

AU - Stanton, Jo Ann L

AU - White, W. Timothy J

AU - Kaplan, Matthew E.

AU - Matisoo-Smith, Elizabeth A.

AU - Adhikarla, Syama

AU - Adler, Christina J.

AU - Balanovska, Elena

AU - Balanovsky, Oleg

AU - Bertranpetit, Jaume

AU - Comas, David

AU - Cooper, Alan

AU - Der Sarkissian, Clio S I

AU - Dulik, Matthew C.

AU - Gaieski, Jill B.

AU - GaneshPrasad, ArunKumar

AU - Haak, Wolfgang

AU - Haber, Marc

AU - Jin, Li

AU - Li, Shilin

AU - Martínez-Cruz, Begoña

AU - Merchant, Nirav C

AU - Mitchell, R. John

AU - Owings, Amanda C.

AU - Parida, Laxmi

AU - Pitchappan, Ramasamy

AU - Platt, Daniel E.

AU - Quintana-Murci, Lluis

AU - Renfrew, Colin

AU - Lacerda, Daniela R.

AU - Royyuru, Ajay K.

AU - Santos, Fabrício R.

AU - Schurr, Theodore G.

AU - Soodyall, Himla

AU - Hernanz, Soria

AU - Swamikrishnan, Pandikumar

AU - Tyler-Smith, Chris

AU - Santhakumari, Arun Varatharajan

AU - Vieira, Pedro Paulo

AU - Vilar, Miguel G.

AU - Zalloua, Pierre A.

AU - Ziegle, Janet S.

AU - Wells, R. Spencer

PY - 2014/1/25

Y1 - 2014/1/25

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KW - 454 sequencing

KW - Bioinformatics

KW - Human

KW - Long-range PCR

KW - Mitochondrial DNA

KW - Next-generation sequencing

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