Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies

Weihong Xu, Hong Gao, Junhee Seok, Julie Wilhelmy, Michael N. Mindrinos, Ronald W. Davis, Wenzhong Xiao

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Large-scale transcriptome profiling in clinical studies often involves assaying multiple samples of a patient to monitor disease progression, treatment effect, and host response in multiple tissues. Such profiling is prone to human error, which often results in mislabeled samples. Here, we present a method to detect mislabeled sample outliers using coding single nucleotide polymorphisms (cSNPs) specifically designed on the microarray and demonstrate that the mislabeled samples can be efficiently identified by either simple clustering of allele-specific expression scores or Mahalanobis distance-based outlier detection method. Based on our results, we recommend the incorporation of cSNPs into future transcriptome array designs as intrinsic markers for sample tracking.

Original languageEnglish
Pages (from-to)386-387
Number of pages2
JournalBioTechniques
Volume52
Issue number6
DOIs
Publication statusPublished - 2012 Jun 1
Externally publishedYes

Fingerprint

Polymorphism
Transcriptome
Single Nucleotide Polymorphism
Nucleotides
Gene Expression Profiling
Microarrays
Cluster Analysis
Disease Progression
Alleles
Tissue
Therapeutics
Clinical Studies

Keywords

  • Coding SNP
  • Microarray
  • Outlier detection
  • Sample tracking
  • Transcriptome profiling

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biotechnology

Cite this

Xu, W., Gao, H., Seok, J., Wilhelmy, J., Mindrinos, M. N., Davis, R. W., & Xiao, W. (2012). Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies. BioTechniques, 52(6), 386-387. https://doi.org/10.2144/0000113879

Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies. / Xu, Weihong; Gao, Hong; Seok, Junhee; Wilhelmy, Julie; Mindrinos, Michael N.; Davis, Ronald W.; Xiao, Wenzhong.

In: BioTechniques, Vol. 52, No. 6, 01.06.2012, p. 386-387.

Research output: Contribution to journalArticle

Xu, W, Gao, H, Seok, J, Wilhelmy, J, Mindrinos, MN, Davis, RW & Xiao, W 2012, 'Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies', BioTechniques, vol. 52, no. 6, pp. 386-387. https://doi.org/10.2144/0000113879
Xu, Weihong ; Gao, Hong ; Seok, Junhee ; Wilhelmy, Julie ; Mindrinos, Michael N. ; Davis, Ronald W. ; Xiao, Wenzhong. / Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies. In: BioTechniques. 2012 ; Vol. 52, No. 6. pp. 386-387.
@article{297dc0ae27fa4827a5908e6493bed583,
title = "Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies",
abstract = "Large-scale transcriptome profiling in clinical studies often involves assaying multiple samples of a patient to monitor disease progression, treatment effect, and host response in multiple tissues. Such profiling is prone to human error, which often results in mislabeled samples. Here, we present a method to detect mislabeled sample outliers using coding single nucleotide polymorphisms (cSNPs) specifically designed on the microarray and demonstrate that the mislabeled samples can be efficiently identified by either simple clustering of allele-specific expression scores or Mahalanobis distance-based outlier detection method. Based on our results, we recommend the incorporation of cSNPs into future transcriptome array designs as intrinsic markers for sample tracking.",
keywords = "Coding SNP, Microarray, Outlier detection, Sample tracking, Transcriptome profiling",
author = "Weihong Xu and Hong Gao and Junhee Seok and Julie Wilhelmy and Mindrinos, {Michael N.} and Davis, {Ronald W.} and Wenzhong Xiao",
year = "2012",
month = "6",
day = "1",
doi = "10.2144/0000113879",
language = "English",
volume = "52",
pages = "386--387",
journal = "BioTechniques",
issn = "0736-6205",
publisher = "Eaton Publishing Company",
number = "6",

}

TY - JOUR

T1 - Coding SNPs as intrinsic markers for sample tracking in large-scale transcriptome studies

AU - Xu, Weihong

AU - Gao, Hong

AU - Seok, Junhee

AU - Wilhelmy, Julie

AU - Mindrinos, Michael N.

AU - Davis, Ronald W.

AU - Xiao, Wenzhong

PY - 2012/6/1

Y1 - 2012/6/1

N2 - Large-scale transcriptome profiling in clinical studies often involves assaying multiple samples of a patient to monitor disease progression, treatment effect, and host response in multiple tissues. Such profiling is prone to human error, which often results in mislabeled samples. Here, we present a method to detect mislabeled sample outliers using coding single nucleotide polymorphisms (cSNPs) specifically designed on the microarray and demonstrate that the mislabeled samples can be efficiently identified by either simple clustering of allele-specific expression scores or Mahalanobis distance-based outlier detection method. Based on our results, we recommend the incorporation of cSNPs into future transcriptome array designs as intrinsic markers for sample tracking.

AB - Large-scale transcriptome profiling in clinical studies often involves assaying multiple samples of a patient to monitor disease progression, treatment effect, and host response in multiple tissues. Such profiling is prone to human error, which often results in mislabeled samples. Here, we present a method to detect mislabeled sample outliers using coding single nucleotide polymorphisms (cSNPs) specifically designed on the microarray and demonstrate that the mislabeled samples can be efficiently identified by either simple clustering of allele-specific expression scores or Mahalanobis distance-based outlier detection method. Based on our results, we recommend the incorporation of cSNPs into future transcriptome array designs as intrinsic markers for sample tracking.

KW - Coding SNP

KW - Microarray

KW - Outlier detection

KW - Sample tracking

KW - Transcriptome profiling

UR - http://www.scopus.com/inward/record.url?scp=84862193766&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84862193766&partnerID=8YFLogxK

U2 - 10.2144/0000113879

DO - 10.2144/0000113879

M3 - Article

VL - 52

SP - 386

EP - 387

JO - BioTechniques

JF - BioTechniques

SN - 0736-6205

IS - 6

ER -