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Apolipoprotein M gene single nucleotide polymorphisms discovery in patients with chronic obstructive pulmonary disease and determined by the base-quenched probe technique

Yu, Yang; Zhang, Jun; Qiao, Yingying; Pan, Lili; Li, Juzhang; Mao, Huihui; Wei, Jiang; Zhang, Xiaoying; Xu, Ning LU and Luo, Guanghua (2017) In Gene 637. p.9-13
Abstract

Background It has been reported increased serum apoM levels seen in the patients suffered from obstructive sleep apnoea and chronic obstructive pulmonary diseases. In the present, we further examine the prevalence of apoM gene SNPs in COPD patients. And a new method base-quenched probe technique is established. Methods In the present study, we first used the Roche 454 GS Junior high-throughput sequencer to analyze 6 COPD samples and 6 control samples, in these samples we found 3 interesting SNPs (rs805264, rs707922 and rs707921) and then we designed primers and probes to establish a simple and quick screening method that is a base-quench probe technique and the genotype was confirmed by melting curves. With this new technique, we... (More)

Background It has been reported increased serum apoM levels seen in the patients suffered from obstructive sleep apnoea and chronic obstructive pulmonary diseases. In the present, we further examine the prevalence of apoM gene SNPs in COPD patients. And a new method base-quenched probe technique is established. Methods In the present study, we first used the Roche 454 GS Junior high-throughput sequencer to analyze 6 COPD samples and 6 control samples, in these samples we found 3 interesting SNPs (rs805264, rs707922 and rs707921) and then we designed primers and probes to establish a simple and quick screening method that is a base-quench probe technique and the genotype was confirmed by melting curves. With this new technique, we further determined 252 COPD samples and 248 normal subjects were applied as controls. Results A total of 19 high-confidence mutations were detected in the Roche 454, 6 mutations among them were not been reported in NCBI, but the mutation frequency was < 20%. Four mutations occurred only in COPD patients, rs751064723 is located in the first exon of transcript 1 and the rest are located in either apoM gene promoter or intron region. The results of melting curve showed that the wild-type and homozygous mutants of rs805264, rs707922 and rs707921 presented melting valley at two different melting temperatures, and the results were consistent with those of DNA sequencing (K = 1, P = 0.000). Conclusions The detection of apoM gene SNPs laid the foundation for the study of the relationship between COPD and apoM, and the base-quenched probe technique is simple, economic and accurate, and it is suitable for a large number of apoM genotyping studies.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
apoM, COPD, Roche/454, SNP
in
Gene
volume
637
pages
5 pages
publisher
Elsevier
external identifiers
  • scopus:85032024588
  • wos:000414115100002
ISSN
0378-1119
DOI
10.1016/j.gene.2017.09.029
language
English
LU publication?
yes
id
4cb03ee3-9031-4091-b58a-a7c531b6675b
date added to LUP
2017-11-02 11:10:17
date last changed
2018-01-16 13:25:17
@article{4cb03ee3-9031-4091-b58a-a7c531b6675b,
  abstract     = {<p>Background It has been reported increased serum apoM levels seen in the patients suffered from obstructive sleep apnoea and chronic obstructive pulmonary diseases. In the present, we further examine the prevalence of apoM gene SNPs in COPD patients. And a new method base-quenched probe technique is established. Methods In the present study, we first used the Roche 454 GS Junior high-throughput sequencer to analyze 6 COPD samples and 6 control samples, in these samples we found 3 interesting SNPs (rs805264, rs707922 and rs707921) and then we designed primers and probes to establish a simple and quick screening method that is a base-quench probe technique and the genotype was confirmed by melting curves. With this new technique, we further determined 252 COPD samples and 248 normal subjects were applied as controls. Results A total of 19 high-confidence mutations were detected in the Roche 454, 6 mutations among them were not been reported in NCBI, but the mutation frequency was &lt; 20%. Four mutations occurred only in COPD patients, rs751064723 is located in the first exon of transcript 1 and the rest are located in either apoM gene promoter or intron region. The results of melting curve showed that the wild-type and homozygous mutants of rs805264, rs707922 and rs707921 presented melting valley at two different melting temperatures, and the results were consistent with those of DNA sequencing (K = 1, P = 0.000). Conclusions The detection of apoM gene SNPs laid the foundation for the study of the relationship between COPD and apoM, and the base-quenched probe technique is simple, economic and accurate, and it is suitable for a large number of apoM genotyping studies.</p>},
  author       = {Yu, Yang and Zhang, Jun and Qiao, Yingying and Pan, Lili and Li, Juzhang and Mao, Huihui and Wei, Jiang and Zhang, Xiaoying and Xu, Ning and Luo, Guanghua},
  issn         = {0378-1119},
  keyword      = {apoM,COPD,Roche/454,SNP},
  language     = {eng},
  month        = {12},
  pages        = {9--13},
  publisher    = {Elsevier},
  series       = {Gene},
  title        = {Apolipoprotein M gene single nucleotide polymorphisms discovery in patients with chronic obstructive pulmonary disease and determined by the base-quenched probe technique},
  url          = {http://dx.doi.org/10.1016/j.gene.2017.09.029},
  volume       = {637},
  year         = {2017},
}