Effects of Inclusion of Relatives in DNA Databases: Empirical Observations from 13K SNPs in Hap-Map Population Data

Saurav Guha, Jianye Ge, Ranajit Chakraborty

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Genome-wide panels of single nucleotide polymorphisms (SNPs) yield a wealth of information that are currently used primarily for detecting genes underlying complex disease phenotypes and quantitative phenotypes. In principle SNPs offer certain operational advantages over short tandem repeats (STRs) for use in human identification. Due to their bi-allelic nature, Linkage Disequilibrium (LD) and lower mutation rate screening of informative SNPs for designing the SNP panel for human forensic identification is a crucial task. Until recently, the screening criteria implemented by researchers vastly ignored the issue of selecting related or unrelated individuals of a population. However, researchers have shown advantages and disadvantages of both type of designing in several ways. In this chapter we have analyzed genome-wide highly polymorphic 13k SNPs of two HapMap populations, e.g., Caucasian and Yoruba, to investigate the extent of basic information that could accumulate by using related or unrelated individuals of same population. Our analysis reveals that Hardy-Weinberg equilibrium (HWE) and allele frequency do not change by using related or unrelated individuals. The use of related individuals also do not provide much extended Linkage Disequilibrium information compared to unrelated individuals of same population. However, allele and genotype sharing significantly differs from related to unrelated individuals. These findings could have a great importance in screening informative SNPs for designing human identification panels.

Original languageEnglish
Title of host publicationHandbook of Statistics
PublisherElsevier B.V.
Pages353-366
Number of pages14
DOIs
StatePublished - 2012

Publication series

NameHandbook of Statistics
Volume28
ISSN (Print)0169-7161

Keywords

  • Allele sharing
  • Forensic genetics
  • Hardy-Weinberg equilibrium
  • Linkage disequilibrium
  • SNP (single nucleotide polymorphism)
  • STR (short tandem repeats)

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    Guha, S., Ge, J., & Chakraborty, R. (2012). Effects of Inclusion of Relatives in DNA Databases: Empirical Observations from 13K SNPs in Hap-Map Population Data. In Handbook of Statistics (pp. 353-366). (Handbook of Statistics; Vol. 28). Elsevier B.V.. https://doi.org/10.1016/B978-0-44-451875-0.00014-2