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Pedigree Analysis

Pedigree Analysis

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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.

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

Eric L Stevens¹, Greg Heckenberg, Joseph D Baugher

¹Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA.

European Journal of Human Genetics : EJHG

|January 26, 2012

Summary

Unexpected relatedness and inbreeding were found in Centre d'Étude du Polymorphisme Humain (CEPH) cell lines, impacting genetic studies. These findings reveal hidden familial connections and homozygosity in reference panels.

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Area of Science:

Human Genetics
Population Genetics
Bioinformatics

Background:

Centre d'Étude du Polymorphisme Humain (CEPH) cell lines are a crucial resource for genetic research, including allele frequency benchmarking, linkage mapping, and gene expression studies.
These multigenerational families are designed as reference panels with known relatedness, primarily consisting of three-generation pedigrees.

Purpose of the Study:

To investigate unexpected relatedness and inbreeding within the CEPH cell line collection using identity-by-state (IBS) and identity-by-descent (IBD) methods.
To benchmark a novel IBD approach (kcoeff) against established software (RELPAIR, PREST).

Main Methods:

Application of identity-by-state (IBS) and identity-by-descent (IBD) analyses to high-density genotype data from 186 CEPH individuals across 13 families.
Utilized the kcoeff software for IBD analysis and benchmarked against RELPAIR and PREST.

Main Results:

Identified significant unexpected relatedness between nominally unrelated grandparents within and between pedigrees, with one pair showing a relatedness coefficient consistent with first-cousins.
Discovered substantial identity-by-descent (IBD2) values in parent-child and second-degree relationships, alongside regions of homozygosity in offspring indicative of inbreeding.
Confirmed findings consistent with previous reports of autozygosity in CEPH families.

Conclusions:

The study reveals previously unrecognized familial relationships and inbreeding within the widely used CEPH reference panels.
These findings necessitate re-evaluation of interpretations from past studies and careful consideration in the design of future genetic research utilizing CEPH resources.
The developed kcoeff method provides a reliable tool for assessing relatedness and inbreeding in genetic datasets.