Improved IBD detection using incomplete haplotype information
1 Department of Mathematics, Dartmouth College, Hanover NH 03755, USA
2 Renal Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston MA 02115, USA
3 Santa Fe Institute, Santa Fe, NM 87501, USA
BMC Genetics 2010, 11:58 doi:10.1186/1471-2156-11-58Published: 30 June 2010
The availability of high density genetic maps and genotyping platforms has transformed human genetic studies. The use of these platforms has enabled population-based genome-wide association studies. However, in inheritance-based studies, current methods do not take full advantage of the information present in such genotyping analyses.
In this paper we describe an improved method for identifying genetic regions shared identical-by-descent (IBD) from recent common ancestors. This method improves existing methods by taking advantage of phase information even if it is less than fully accurate or missing. We present an analysis of how using phase information increases the accuracy of IBD detection compared to using only genotype information.
Our algorithm should have utility in a wide range of genetic studies that rely on identification of shared genetic material in large families or small populations.