title: SAQC: SNP array quality control.
abstract: BACKGROUND
  Genome-wide single-nucleotide polymorphism (SNP) arrays containing hundreds of thousands of SNPs from the human genome have proven useful for studying important human genome questions. Data quality of SNP arrays plays a key role in the accuracy and precision of downstream data analyses. However, good indices for assessing data quality of SNP arrays have not yet been developed.
  
  
  RESULTS
  We developed new quality indices to measure the quality of SNP arrays and/or DNA samples and investigated their statistical properties. The indices quantify a departure of estimated individual-level allele frequencies (AFs) from expected frequencies via standardized distances. The proposed quality indices followed lognormal distributions in several large genomic studies that we empirically evaluated. AF reference data and quality index reference data for different SNP array platforms were established based on samples from various reference populations. Furthermore, a confidence interval method based on the underlying empirical distributions of quality indices was developed to identify poor-quality SNP arrays and/or DNA samples. Analyses of authentic biological data and simulated data show that this new method is sensitive and specific for the detection of poor-quality SNP arrays and/or DNA samples.
  
  
  CONCLUSIONS
  This study introduces new quality indices, establishes references for AFs and quality indices, and develops a detection method for poor-quality SNP arrays and/or DNA samples. We have developed a new computer program that utilizes these methods called SNP Array Quality Control (SAQC). SAQC software is written in R and R-GUI and was developed as a user-friendly tool for the visualization and evaluation of data quality of genome-wide SNP arrays. The program is available online (http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm).
authors.affiliation: Institute of Statistical Science, Academia Sinica, Taipei, Taiwan. hsinchou@stat.sinica.edu.tw
authors.forename: Hsin-Chou
authors.initials: HC
authors.lastname: Yang
authors.forename: Hsin-Chi
authors.initials: HC
authors.lastname: Lin
authors.forename: Meijyh
authors.initials: M
authors.lastname: Kang
authors.forename: Chun-Houh
authors.initials: CH
authors.lastname: Chen
authors.forename: Chien-Wei
authors.initials: CW
authors.lastname: Lin
authors.forename: Ling-Hui
authors.initials: LH
authors.lastname: Li
authors.forename: Jer-Yuarn
authors.initials: JY
authors.lastname: Wu
authors.forename: Yuan-Tsong
authors.initials: YT
authors.lastname: Chen
authors.forename: Wen-Harn
authors.initials: WH
authors.lastname: Pan
mesh_terms: D004247:DNA / Q000032:analysis; D005787:Gene Frequency; D015894:Genome, Human; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control
chemical_list: D004247:DNA