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

Abstract

A set of Centre d'Étude 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.

Figure 1

Relationships among CEPH three-generation pedigree members based on IBS and IBD measurements. (a) IBS2^*_ratio plot annotated by relationships. Each data point corresponds to a comparison of two individuals based on genotype data. The IBS2^*_ratio consisted of autosome-wide (IBS2^*/(IBS0+IBS2^*)) on the x-axis measured against kcoeff's K1 (level of genome shared IBD1) on the y-axis. Clusters were expected (based on prior sample annotation) of identical, parent–child, full-siblings, 1/4 sharing (ie, AV and GG), and unrelated individuals. We also observed pairs of samples having x-axis values consistent with distant relatedness (eg, arrows 1 and 2). (b) IBS2^*_ratio (x-axis) versus kcoeff's K2 (level of genome-shared IBD2; y-axis), annotated by relationships. (c) IBS2^*_ratio (x-axis) versus kcoeff's K0 (level of genome shared IBD0; y-axis).

Figure 2

Inbreeding in a CEPH/Amish pedigree. For all panels, data for chromosome 6 are shown based on SNPduo analyses. Upper three panels: (a) pairwise IBS patterns are presented for parents NA13113 and NA13114. Note regions 1 and 8 in which an absence of IBS0 is shown. Region 5 corresponds to regions 6 and 7 (panels b and c) and represents two individuals with different stretches of homozygosity (lack of AB calls) compared with each other; whereas both were homozygous, the differences were evident from the occurrence of IBS0 in the region 5. (b) Genotypes of NA13113. Note homozygosity in region 6. (c) Genotypes of NA13114. Note homozygosity in region 7. (d) Pairwise IBS patterns for NA13117 and NA13127 (children of NA13113 and NA13114). Note that region 2 indicates IBD2 between the siblings NA13117 and NA13127 and overlaps a region of inferred IBD1 between the parents (region 1). (e) Genotypes for NA13117. Note that regions 3 and 9 are homozygous segments that correspond to a lack of IBS0 in regions 1 and 8 from panel A; this suggests consanguinity. (f) Genotypes of NA13127. Region 4 is a homozygous segment that corresponds to region 1 and is identical to region 3. This supports consanguinity due to lack of IBS0 between the parents (a).

Figure 3

Revised CEPH pedigrees. Curved lines denote significant relatedness between pairs of individuals with estimated autosome-wide K1 and pIBD1 values indicated in Table 2. Dashed rectangles correspond to pedigrees as given on the Coriell Cell Repositories website, except that CEPH/Venezuelan pedigrees 102 and 104 had not previously been explicitly presented as a single pedigree visually. Numbers given on the pedigrees for individuals correspond to standard Coriell designations (eg, 11930 corresponds to cell line GM11930 or DNA sample NA11930). (a) CEPH/Utah pedigrees 1331 and 1424 were interrelated based on K1 sharing between grandmother NA07050 and grandfather NA11932 on chromosome 4. Additionally, a significant K1 value was estimated between paternal grandmother NA11931 and maternal grandmother NA11933 in CEPH/Utah pedigree 1424. (b) CEPH/Utah pedigree 1427 had significantly elevated K1 between NA12977 and NA12978 and marginal K1 between all four grandparents supported by homozygosity and SNPduo analysis (see Materials and Methods). (c) CEPH/Venezuelan families 102 and 104 include numerous AV relationships. All four grandparents displayed elevated K1 levels. (d) CEPH/Utah pedigree 1582 had minimal K1 levels associated with homozygosity between NA12921 and NA12924 (supported by SNPduo analysis). (e) CEPH/Amish pedigree 884 was characterized by four grandparents with elevated K1 levels. (f) CEPH/Utah pedigree 1356 had minimal K1 levels also associated with homozygosity and supported by SNPduo analysis. ^*Indicates the presence of homozygosity due to autozygosity; ^#indicates the presence of multiple regions; any number within a square or circle indicates a unique chromosome in which relatedness or homozygosity was present; ^@indicates the members of CEPH/Venezuelan pedigree 104 within the combined CEPH/Venezuelan pedigrees 102 and 104.

Figure 4

Comparison of kcoeff to PREST and RELPAIR for k1 and k2, and comparison of kcoeff and PREST for k0. An IBS2^*_ratio is plotted as a function of varying IBD estimates annotated by RELPAIR for k1 and k2 estimates with a comparison of k0 between kcoeff and PREST in parent–child relationships. (a) K2 (kcoeff) estimates of true AV, GG, and parent–child relationships incorrectly assigned a FS annotation from RELPAIR. Note the positive relationship between level of K2 and number per 25 trials of RELPAIR FS annotation. The color scale for panels a and b includes black (no RELPAIR FS calls) and ranges from blue (1 FS call per 25 trials) to red (25/25 FS calls). (b) pIBD2 (PREST) estimates of relationships incorrectly assigned a FS annotation from RELPAIR. (c) K1 estimates of unrelated and distantly related individuals assigned a CO annotation from RELPAIR. Note the positive relationship between level of K1 and number per 25 trials of CO annotation. (d) pIBD1 estimates of unrelated and distantly related individuals assigned a CO annotation from RELPAIR. (e) K0 estimates in parent–child relationships with selected pairs being identified. (f) pIBD0 estimates in parent–child relationships with selected pairs highlighted. Note the discrepancies between panels e and f. Also note that as there were duplicate samples present, it was not possible to fully annotate all relationships (see arrow 1 in panel f). The x and y-axis scales are the same for panels a/b, c/d, and e/f. Arrows indicate specific pairwise comparisons (see text for details).