title: Two algorithms for biospecimen comparison and differentiation using SNP genotypes.
abstract: OBJECTIVE
  Biobanks are frequently required to verify specimen relationships. We present two algorithms to compare SNP genotype patterns that provide an objective, high-throughput tool for verification.
  
  
  METHODS
  The first algorithm allows for comparison of all holdings within a biobank, and is well suited to construct sample relationships de novo for comparison with assumed relationships. The second algorithm is tailored to oncology, and allows one to confirm that paired DNAs from malignant and normal tissues are from the same individual in the presence of copy number variations. To evaluate both algorithms, we used an internal training data set (n = 1504) and an external validation data set (n = 1457).
  
  
  RESULTS
  In comparison with the results from manual review and a priori knowledge of patient relationships, we identified no errors in interpreting sample relationships within our validation data set.
  
  
  CONCLUSIONS
  We provide an efficient and objective method of automated data analysis that is currently lacking for establishing and verifying specimen relationships in biobanks.
authors: International Genomics Consortium, Suite 300, 445 North 5th Street, Phoenix, AZ 85004, USA. smorris@intgen.org
authors: Scott
authors: S
authors: Morris
authors: Esma S
authors: ES
authors: Gel
authors: Jordan V
authors: JV
authors: Smith
authors: Joseph D
authors: JD
authors: Paulauskis
authors: Dirk van den
authors: Dv
authors: Boom
authors: Paul
authors: P
authors: Oeth
authors: Robert
authors: R
authors: Penny
mesh_terms: D000465:Algorithms; D018070:Biological Specimen Banks; D056915:DNA Copy Number Variations / Q000235:genetics*; D060005:Genotyping Techniques; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software