Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics

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Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics. / Mikkelsen, Martin; Frank-Hansen, Rune; Hansen, Anders Johannes; Morling, Niels.

I: Forensic science international. Genetics, Bind 12, 09.2014, s. 30-37.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt

Harvard

Mikkelsen, M, Frank-Hansen, R, Hansen, AJ & Morling, N 2014, 'Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics', Forensic science international. Genetics, bind 12, s. 30-37. https://doi.org/10.1016/j.fsigen.2014.03.014

APA

Mikkelsen, M., Frank-Hansen, R., Hansen, A. J., & Morling, N. (2014). Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics. Forensic science international. Genetics, 12, 30-37. https://doi.org/10.1016/j.fsigen.2014.03.014

Vancouver

Mikkelsen M, Frank-Hansen R, Hansen AJ, Morling N. Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics. Forensic science international. Genetics. 2014 sep.;12:30-37. https://doi.org/10.1016/j.fsigen.2014.03.014

Author

Mikkelsen, Martin ; Frank-Hansen, Rune ; Hansen, Anders Johannes ; Morling, Niels. / Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics. I: Forensic science international. Genetics. 2014 ; Bind 12. s. 30-37.

Bibtex

@article{c5948ed885f54c579763d84ca4a85bf4,

title = "Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics",

abstract = "RESULTS: of sequencing of whole mitochondrial genome, HV1 and HV2 DNA with the second generation system (SGS) Roche 454 GS Junior were compared with results of Sanger sequencing and SNP typing with SNaPshot single base extension detected with MALDI-TOF and capillary electrophoresis. We investigated the performance of the software analysis of the data, reproducibility, ability to sequence homopolymeric regions, detection of mixtures and heteroplasmy as well as the implications of the depth of coverage. We found full reproducibility between samples sequenced twice with SGS. We found close to full concordance between the mtDNA sequences of 26 samples obtained with (1) the 454 SGS method using a depth of coverage above 100 and (2) Sanger sequencing and SNP typing. The discrepancies were primarily observed in homopolymeric regions. The 454 SGS method was able to sequence 95% of the reads correctly in homopolymers up to 4 bases, and up to 6 bases could be sequenced with similar success if the results were carefully, visually inspected. The 454 technology was able to detect mixtures or heteroplasmy of approximately 10%. We detected previously unreported heteroplasmy in the GM9947A component of the NIST human mitochondrial DNA SRM-2392 standard reference material.",

author = "Martin Mikkelsen and Rune Frank-Hansen and Hansen, {Anders Johannes} and Niels Morling",

year = "2014",

month = sep,

doi = "10.1016/j.fsigen.2014.03.014",

language = "English",

volume = "12",

pages = "30--37",

journal = "Forensic Science International: Genetics",

issn = "1872-4973",

publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics

AU - Mikkelsen, Martin

AU - Frank-Hansen, Rune

AU - Hansen, Anders Johannes

AU - Morling, Niels

PY - 2014/9

Y1 - 2014/9

N2 - RESULTS: of sequencing of whole mitochondrial genome, HV1 and HV2 DNA with the second generation system (SGS) Roche 454 GS Junior were compared with results of Sanger sequencing and SNP typing with SNaPshot single base extension detected with MALDI-TOF and capillary electrophoresis. We investigated the performance of the software analysis of the data, reproducibility, ability to sequence homopolymeric regions, detection of mixtures and heteroplasmy as well as the implications of the depth of coverage. We found full reproducibility between samples sequenced twice with SGS. We found close to full concordance between the mtDNA sequences of 26 samples obtained with (1) the 454 SGS method using a depth of coverage above 100 and (2) Sanger sequencing and SNP typing. The discrepancies were primarily observed in homopolymeric regions. The 454 SGS method was able to sequence 95% of the reads correctly in homopolymers up to 4 bases, and up to 6 bases could be sequenced with similar success if the results were carefully, visually inspected. The 454 technology was able to detect mixtures or heteroplasmy of approximately 10%. We detected previously unreported heteroplasmy in the GM9947A component of the NIST human mitochondrial DNA SRM-2392 standard reference material.

AB - RESULTS: of sequencing of whole mitochondrial genome, HV1 and HV2 DNA with the second generation system (SGS) Roche 454 GS Junior were compared with results of Sanger sequencing and SNP typing with SNaPshot single base extension detected with MALDI-TOF and capillary electrophoresis. We investigated the performance of the software analysis of the data, reproducibility, ability to sequence homopolymeric regions, detection of mixtures and heteroplasmy as well as the implications of the depth of coverage. We found full reproducibility between samples sequenced twice with SGS. We found close to full concordance between the mtDNA sequences of 26 samples obtained with (1) the 454 SGS method using a depth of coverage above 100 and (2) Sanger sequencing and SNP typing. The discrepancies were primarily observed in homopolymeric regions. The 454 SGS method was able to sequence 95% of the reads correctly in homopolymers up to 4 bases, and up to 6 bases could be sequenced with similar success if the results were carefully, visually inspected. The 454 technology was able to detect mixtures or heteroplasmy of approximately 10%. We detected previously unreported heteroplasmy in the GM9947A component of the NIST human mitochondrial DNA SRM-2392 standard reference material.

U2 - 10.1016/j.fsigen.2014.03.014

DO - 10.1016/j.fsigen.2014.03.014

M3 - Journal article

C2 - 24879032

VL - 12

SP - 30

EP - 37

JO - Forensic Science International: Genetics

JF - Forensic Science International: Genetics

SN - 1872-4973

ER -

ID: 113673824