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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0
BMC Research Notes, Volume 4, Article 426, Year 2011
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Description
Background: Developments in DNA resequencing microarrays include mitochondrial DNA (mtDNA) sequencing and mutation detection. Failure by the microarray to identify a base, compared to the reference sequence, is designated an 'N-call.' This study re-examined the N-call distribution of mtDNA samples sequenced by the Affymetrix MitoChip v.2.0, based on the hypothesis that N-calls may represent insertions or deletions (indels) in mtDNA. Findings. We analysed 16 patient mtDNA samples using MitoChip. N-calls by the proprietary GSEQ software were significantly reduced when either of the freeware on-line algorithms ResqMi or sPROFILER was utilized. With sPROFILER, this decrease in N-calls had no effect on the homoplasmic or heteroplasmic mutation levels compared to GSEQ software, but ResqMi produced a significant change in mutation load, as well as producing longer N-cell stretches. For these reasons, further analysis using ResqMi was not attempted. Conventional DNA sequencing of the longer N-calls stretches from sPROFILER revealed 7 insertions and 12 point mutations. Moreover, analysis of single-base N-calls of one mtDNA sample found 3 other point mutations. Conclusions: Our study is the first to analyse N-calls produced from GSEQ software for the MitoChipv2.0. By narrowing the focus to longer stretches of N-calls revealed by sPROFILER, conventional sequencing was able to identify unique insertions and point mutations. Shorter N-calls also harboured point mutations, but the absence of deletions among N-calls suggests that probe confirmation affects binding and thus N-calling. This study supports the contention that the GSEQ is more capable of assigning bases when used in conjunction with sPROFILER. © 2011 Duley et al; licensee BioMed Central Ltd.
Authors & Co-Authors
Zamzami, Mazin Abdulaziz
Australia, Brisbane
The University of Queensland
Saudi Arabia, Jeddah
King Abdulaziz University
Price, Gareth R.
Australia, Brisbane
Mater Health Services Brisbane
Taylor, Robert William
United Kingdom, Newcastle
University of Newcastle Upon Tyne, Faculty of Medical Sciences
Blakely, Emma L.
United Kingdom, Newcastle
University of Newcastle Upon Tyne, Faculty of Medical Sciences
Oancea, Iulia
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Mater Medical Research Institute
Bowling, Francis Gerard
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Mater Medical Research Institute
Duley, John A.
Australia, Brisbane
The University of Queensland
Australia, Brisbane
Mater Medical Research Institute
Statistics
Citations: 7
Authors: 7
Affiliations: 5
Identifiers
Doi:
10.1186/1756-0500-4-426
Research Areas
Cancer
Genetics And Genomics
Health System And Policy