Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland: Scottish Family Health Study

Shona M Kerr, Archie Campbell, Lee Murphy, Caroline Hayward, Cathy Jackson, Louise V Wain, Martin D Tobin, Anna Dominiczak, Andrew Morris, Blair H Smith, David J Porteous

Research output: Contribution to journalArticlepeer-review

Abstract

Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based biobank of 24,000 participants with rich phenotype and DNA available for genetic research. This paper describes the laboratory results from genotyping 32 single nucleotide polymorphisms (SNPs) on DNA from over 10,000 participants who attended GS:SFHS research clinics. The analysis described here was undertaken to test the quality of genetic information available to researchers. The success rate of each marker genotyped (call rate), minor allele frequency and adherence to Mendelian inheritance are presented. The few deviations in marker transmission in the 925 parent-child trios analysed were assessed as to whether they were likely to be miscalled genotypes, data or sample handling errors, or pedigree inaccuracies including non-paternity.
Original languageEnglish
Article number38
Number of pages7
JournalBMC Medical Genetics
Volume14
Issue number1
DOIs
Publication statusPublished - 22 Mar 2013

Keywords

  • Pedigree
  • Family Characteristics
  • Polymorphism, Single Nucleotide
  • Humans
  • Aged
  • Child
  • Sequence Analysis, DNA
  • Research Design
  • Genotype
  • Scotland
  • Adult
  • Cohort Studies
  • DNA
  • Family
  • Middle Aged
  • Sample Size
  • Parents
  • Family Health
  • Female
  • Male

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