About: Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0 Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0
Creator	Bowling, Francis Oancea, Iulia Blakely, Emma Duley, John Price, Gareth »more»
topic	covid:c6518c58374cc315647f2873a234cfa983746bfd#this
source	Medline; PMC
abstract	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.
has issue date	2011-10-20(xsd:dateTime)
bibo:doi	10.1186/1756-0500-4-426
bibo:pmid	22011414
has license	cc-by
sha1sum (hex)	c6518c58374cc315647f2873a234cfa983746bfd
schema:url	https://doi.org/10.1186/1756-0500-4-426
resource representing a document's title	Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0
has PubMed Central identifier	PMC3208482
has PubMed identifier	22011414
schema:publication	BMC Res Notes
resource representing a document's body	covid:c6518c58374cc315647f2873a234cfa983746bfd#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/c6518c58374cc315647f2873a234cfa983746bfd
is schema:about of	named entity 'stretches' named entity 'Our' named entity 'revealed' named entity 'Affymetrix' named entity 'sequencing' »more»

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2025 OpenLink Software