Editing Identity by descent (section)

=== IBD mapping ===
IBD mapping<ref name=" Albrechtsen.2009"/> is similar to linkage analysis, but can be performed without a known pedigree on a cohort of unrelated individuals. IBD mapping can be seen as a new form of association analysis that increases the [[Statistical power|power]] to map genes or genomic regions containing multiple rare disease susceptibility variants.<ref name="Purcell.2007"/><ref name="Browning.2012b">{{Cite journal
| last1 = Browning | first1 = S. R.
| last2 = Thompson | first2 = E. A.  | author2-link = Elizabeth A. Thompson
| doi = 10.1534/genetics.111.136937
| title = Detecting Rare Variant Associations by Identity-by-Descent Mapping in Case-Control Studies
| journal = Genetics
| volume = 190
| issue = 4
| pages = 1521–1531
| year = 2012
| pmid = 22267498
| pmc =3316661
}}</ref>

Using simulated data, Browning and [[Elizabeth A. Thompson|Thompson]] showed that IBD mapping has higher power than association testing when multiple rare variants within a gene contribute to disease susceptibility.<ref name="Browning.2012b"/> Via IBD mapping, genome-wide [[Statistical significance|significant]] regions in isolated populations as well as outbred populations were found while standard association tests failed.<ref name="Gusev.2012"/><ref name="Gusev.2011">{{Cite journal
| last1 = Gusev | first1 = A.
| last2 = Kenny | first2 = E. E.
| last3 = Lowe | first3 = J. K.
| last4 = Salit | first4 = J.
| last5 = Saxena | first5 = R.
| last6 = Kathiresan | first6 = S.
| last7 = Altshuler | first7 = D. M.
| last8 = Friedman | first8 = J. M.
| last9 = Breslow | first9 = J. L.
| last10 = Pe'Er | first10 = I.
| doi = 10.1016/j.ajhg.2011.04.023
| title = DASH: A Method for Identical-by-Descent Haplotype Mapping Uncovers Association with Recent Variation
| journal = The American Journal of Human Genetics
| volume = 88
| issue = 6
| pages = 706–717
| year = 2011
| pmid = 21620352
| pmc =3113343
}}</ref> Houwen et al. used IBD sharing to identify the chromosomal location of a gene responsible for benign recurrent intrahepatic [[cholestasis]] in an isolated fishing population.<ref name="Houwen.1994">{{Cite journal
| last1 = Houwen | first1 = R. H. J.
| last2 = Baharloo | first2 = S.
| last3 = Blankenship | first3 = K.
| last4 = Raeymaekers | first4 = P.
| last5 = Juyn | first5 = J.
| last6 = Sandkuijl | first6 = L. A.
| last7 = Freimer | first7 = N. B.
| doi = 10.1038/ng1294-380
| title = Genome screening by searching for shared segments: Mapping a gene for benign recurrent intrahepatic cholestasis
| journal = Nature Genetics
| volume = 8
| issue = 4
| pages = 380–386
| year = 1994
| pmid = 7894490
| pmc =
| hdl = 1765/55192
| s2cid = 8131209
| url = http://repub.eur.nl/pub/55192
| hdl-access = free
}}</ref> Kenny et al. also used an isolated population to fine-map a signal found by a [[genome-wide association study]] (GWAS) of plasma [[plant sterol]] (PPS) levels, a surrogate measure of cholesterol absorption from the intestine.<ref name="Kenny.2009">{{Cite journal
| last1 = Kenny | first1 = E. E.
| last2 = Gusev | first2 = A.
| last3 = Riegel | first3 = K.
| last4 = Lutjohann | first4 = D.
| last5 = Lowe | first5 = J. K.
| last6 = Salit | first6 = J.
| last7 = Maller | first7 = J. B.
| last8 = Stoffel | first8 = M.
| last9 = Daly | first9 = M. J.
| last10 = Altshuler | first10 = D. M.
| last11 = Friedman | first11 = J. M.
| last12 = Breslow | first12 = J. L.
| last13 = Pe'Er | first13 = I.
| last14 = Sehayek | first14 = E.
| title = Systematic haplotype analysis resolves a complex plasma plant sterol locus on the Micronesian Island of Kosrae
| doi = 10.1073/pnas.0907336106
| journal = Proceedings of the National Academy of Sciences
| volume = 106
| issue = 33
| pages = 13886–13891
| year = 2009
| pmid = 19667188
| pmc =2728990
| bibcode = 2009PNAS..10613886K
| doi-access = free
}}</ref> Francks et al. was able to identify a potential susceptibility locus for [[schizophrenia]] and [[bipolar disorder]] with genotype data of case-control samples.<ref name="Francks.2008">{{Cite journal
| last1 = Francks | first1 = C.
| last2 = Tozzi | first2 = F.
| last3 = Farmer | first3 = A.
| last4 = Vincent | first4 = J. B.
| last5 = Rujescu | first5 = D.
| last6 = St Clair | first6 = D.
| last7 = Muglia | first7 = P.
| doi = 10.1038/mp.2008.100
| title = Population-based linkage analysis of schizophrenia and bipolar case–control cohorts identifies a potential susceptibility locus on 19q13
| journal = Molecular Psychiatry
| volume = 15
| issue = 3
| pages = 319–325
| year = 2008
| pmid = 18794890
| pmc =
| doi-access = free
| hdl = 11858/00-001M-0000-0012-C935-9
| hdl-access = free
}}</ref> Lin et al. found a genome-wide significant linkage signal in a dataset of [[multiple sclerosis]] patients.<ref name="Lin.2013">{{Cite journal
| last1 = Lin | first1 = R.
| last2 = Charlesworth | first2 = J.
| last3 = Stankovich | first3 = J.
| last4 = Perreau | first4 = V. M.
| last5 = Brown | first5 = M. A.
| last6 = Anzgene | first6 = B. V.
| last7 = Taylor | first7 = B. V.
| editor1-last = Toland
| editor1-first = Amanda Ewart
| title = Identity-by-Descent Mapping to Detect Rare Variants Conferring Susceptibility to Multiple Sclerosis
| doi = 10.1371/journal.pone.0056379
| journal = PLOS ONE
| volume = 8
| issue = 3
| pages = e56379
| year = 2013
| pmid = 23472070
| pmc =3589405
| bibcode = 2013PLoSO...856379L
| doi-access = free
}}</ref> Letouzé et al. used IBD mapping to look for [[founder mutation]]s in [[cancer]] samples.<ref name="Letouze.2012">{{Cite journal
| last1 = Letouzé | first1 = E.
| last2 = Sow | first2 = A.
| last3 = Petel | first3 = F.
| last4 = Rosati | first4 = R.
| last5 = Figueiredo | first5 = B. C.
| last6 = Burnichon | first6 = N.
| last7 = Gimenez-Roqueplo | first7 = A. P.
| last8 = Lalli | first8 = E.
| last9 = De Reyniès | first9 = A. L.
| editor1-last = Mailund
| editor1-first = Thomas
| title = Identity by Descent Mapping of Founder Mutations in Cancer Using High-Resolution Tumor SNP Data
| doi = 10.1371/journal.pone.0035897
| journal = PLOS ONE
| volume = 7
| issue = 5
| pages = e35897
| year = 2012
| pmid = 22567117
| pmc =3342326
| bibcode = 2012PLoSO...735897L
| doi-access = free
}}</ref>

[[File:IBD segment detected by HapFABIA in 1000Genomes.png|thumb|upright=2.0|alt=An IBD segment identified by HapFABIA in the 1000 Genomes|An IBD segment identified by HapFABIA in Asian genomes. Rare single nucleotide variants (SNVs) that tag the IBD segment are coloured purple. Below the turquoise bar, the IBD segment in ancient genomes is displayed.]]