TY - GEN
T1 - Pedigree Reconstruction Using Identity by Descent
AU - Kirkpatrick, Bonnie
AU - Li, Shuai Cheng
AU - Karp, Richard M.
AU - Halperin, Eran
N1 - Publisher Copyright:
© 2011, Springer-Verlag Berlin Heidelberg.
PY - 2011
Y1 - 2011
N2 - Can we find the family trees, or pedigrees, that relate the haplotypes of a group of individuals? Collecting the genealogical information for how individuals are related is a very time-consuming and expensive process. Methods for automating the construction of pedigrees could stream-line this process. While constructing single-generation families is relatively easy given whole genome data, reconstructing multi-generational, possibly inbred, pedigrees is much more challenging. This paper addresses the important question of reconstructing monogamous, regular pedigrees, where pedigrees are regular when individuals mate only with other individuals at the same generation. This paper introduces two multi-generational pedigree reconstruction methods: one for inbreeding relationships and one for outbreeding relationships. In contrast to previous methods that focused on the independent estimation of relationship distances between every pair of typed individuals, here we present methods that aim at the reconstruction of the entire pedigree. We show that both our methods out-perform the state-of-the-art and that the outbreeding method is capable of reconstructing pedigrees at least six generations back in time with high accuracy. The two programs are available at http://cop.icsi.berkeley.edu/ cop.
AB - Can we find the family trees, or pedigrees, that relate the haplotypes of a group of individuals? Collecting the genealogical information for how individuals are related is a very time-consuming and expensive process. Methods for automating the construction of pedigrees could stream-line this process. While constructing single-generation families is relatively easy given whole genome data, reconstructing multi-generational, possibly inbred, pedigrees is much more challenging. This paper addresses the important question of reconstructing monogamous, regular pedigrees, where pedigrees are regular when individuals mate only with other individuals at the same generation. This paper introduces two multi-generational pedigree reconstruction methods: one for inbreeding relationships and one for outbreeding relationships. In contrast to previous methods that focused on the independent estimation of relationship distances between every pair of typed individuals, here we present methods that aim at the reconstruction of the entire pedigree. We show that both our methods out-perform the state-of-the-art and that the outbreeding method is capable of reconstructing pedigrees at least six generations back in time with high accuracy. The two programs are available at http://cop.icsi.berkeley.edu/ cop.
UR - http://www.scopus.com/inward/record.url?scp=79953169472&partnerID=8YFLogxK
U2 - 10.1007/978-3-642-20036-6_15
DO - 10.1007/978-3-642-20036-6_15
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AN - SCOPUS:79953169472
SN - 9783642200359
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 136
EP - 152
BT - Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings
A2 - Bafna, Vineet
A2 - Sahinalp, S. Cenk
PB - Springer Verlag
T2 - 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011
Y2 - 28 March 2011 through 31 March 2011
ER -