Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us?

Leutenegger, Anne-Louise; Sahbatou, Mourad; Gazal, Steven; Cann, Howard M.; Génin, Emmanuelle

doi:10.1038/ejhg.2010.205

Cited by 52 publications

(63 citation statements)

References 27 publications

(26 reference statements)

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“…This allowed us to obtain a more accurate estimation of the level of inbreeding in the Lebanese population. 6 In previous studies, F was estimated using Malécot's formula applied to sociological data from first cousin unions. Based on the assumption that 25% of marriages occur between first cousins, F was found to be equal to 1.56%.…”

Section: Discussionmentioning

confidence: 99%

“…3,[7][8][9] Using biological methodologies, an F estimation was first calculated using a microsatellite panel and FEstim algorithm and was then improved using genome-wide single-nucleotide polymorphism (SNP) chip-based advanced algorithms. 5,6 These estimations were based on the genotyping of a large number of genetic markers to infer the individual genomic proportion that is homozygous by descent (HBD). Two parameters were then calculated; the proportion of genomic HBD and the average length of the HBD segments, which are the indicators of the inbreeding and the age of common ancestors, respectively.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide inbreeding estimation within Lebanese communities using SNP arrays

et al. 2014

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Consanguineous marriages have been widely practiced in several global communities with varying rates depending on religion, culture, and geography. In consanguineous marriages, parents pass to their children autozygous segments known as homozygous by descent segments. In this study, single-nucleotide polymorphisms were analyzed in 165 unrelated Lebanese people from Greek Orthodox, Maronite, Shiite and Sunni communities. Runs of homozygosity, total inbreeding levels, remote consanguinity, and population admixture and structure were estimated. The inbreeding coefficient value was estimated to be 1.61% in offspring of unrelated parents over three generations and 8.33% in offspring of first cousins. From these values, remote consanguinity values, resulting from genetic drift or recurrent consanguineous unions, were estimated in offspring of unrelated and first-cousin parents to be 0.61 and 1.2%, respectively. This remote consanguinity value suggests that for any unrelated marriages in Lebanon, the mates could be related as third cousins or as second cousins once removed. Under the assumption that 25% of marriages occur between first cousins, the mean inbreeding value of 2.3% may explain the increased incidence of recessive disease in offspring. Our analysis reveals a common ancestral population in the four Lebanese communities we studied.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-wide inbreeding estimation within Lebanese communities using SNP arrays

et al. 2014

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“…The geographic location of genetic isolates in Argentina in the clusters with high random consanguinity highlights the usefulness of this approach in identifying isolates with reduced genetic heterogeneity and reduced effective population size. Since the occurrence of rare Mendelian diseases is common in some isolates, their identification, such as selection of candidate populations to be molecularly studied is made (Leutenegger et al 2011), also has great health care relevance.…”

Section: Discussionmentioning

confidence: 99%

“…consang.net). More recently, relying on genomic data, Leutenegger et al (2011) estimated the inbreeding levels and mating-type proportions in 52 populations from all continents. They found that consanguinity was present in almost all populations with the highest rates of inbreeding in North Africa, the Middle East, and Central South Asia.…”

Section: Introductionmentioning

confidence: 99%

Random inbreeding, isonymy, and population isolates in Argentina

et al. 2014

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“…Recently, evidence for inbreeding was established within a subset of the HGDP-CEPH panel. 11 A variety of methods are available to determine relatedness between individuals based on genotype data. We adopted three complementary approaches.…”

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confidence: 99%

Consanguinity in Centre d’Étude du Polymorphisme Humain (CEPH) pedigrees

et al. 2012

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A set of Centre d'É tude du Polymorphisme Humain (CEPH) cell lines serves as a large reference collection that has been widely used as a benchmark for allele frequencies in the analysis of genetic variants, to create linkage maps of the human genome, to study the genetics of gene expression, to provide samples to the HapMap and 1000 Genomes projects, and for a variety of other applications. An explicit feature of the CEPH collection is that these multigenerational families represent reference panels of known relatedness, consisting mostly of three-generation pedigrees with large sibships, two parents, and grandparents. We applied identity-by-state (IBS) and identity-by-descent (IBD) methods to high-density genotype data from 186 CEPH individuals in 13 families. We identified unexpected relatedness between nominally unrelated grandparents both within and between pedigrees. For one pair, the estimated Cotterman coefficient of relatedness k1 exceeded 0.2, consistent with one-eighth sharing (eg, first-cousins). Unexpectedly, significant IBD2 values were discovered in both second-degree and parent-child relationships. These were accompanied by regions of homozygosity in the offspring, which corresponded to blocks lacking IBS0 in purportedly unrelated parents, consistent with inbreeding. Our findings support and extend a 1999 report, based on the use of short tandem-repeat polymorphisms, that several CEPH families had regions of homozygosity consistent with autozygosity. We benchmarked our IBD approach (called kcoeff) against both RELPAIR and PREST software packages. Our findings may affect the interpretation of previous studies and the design of future studies that rely on the CEPH resource.

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Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us?

Cited by 52 publications

References 27 publications

Genome-wide inbreeding estimation within Lebanese communities using SNP arrays

Genome-wide inbreeding estimation within Lebanese communities using SNP arrays

Random inbreeding, isonymy, and population isolates in Argentina

Consanguinity in Centre d’Étude du Polymorphisme Humain (CEPH) pedigrees

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