Inbreeding Loops Research Articles

Investigation of the association of the MLPH gene with seasonal canine flank alopecia in Rhodesian Ridgeback dogs

BackgroundCanine flank alopecia (CFA) is a skin condition in dogs characterized by non-inflammatory, seasonally recurring episodes of localized hair loss and often hyperpigmentation of the affected skin. A genetic basis is suspected because of the predisposition in certain breeds, such as the Rhodesian Ridgeback (RR). This study investigated the possible role of the canine melanophylin (MLPH) gene in CFA among RRs through pedigree analysis and MLPH genotyping.ResultsWe included 24 CFA-affected and 12 non-CFA-affected control RRs. Pedigree analysis revealed inbreeding loops and close family relationships among the CFA-affected dogs, indicating the potential heritability of CFA. MLPH genotyping revealed 3/24 (12.5%) affected dogs and 1/12 (8.3%) control dogs to be heterozygous (Dd) for the dilute (d) allele, indicating no difference between these groups. None of the dogs were found to be homozygous (dd). Statistical analysis did not reveal an association between the MLPH-d allele and CFA.ConclusionsThe familial patterns among affected RRs observed through pedigree analysis suggest a potential genetic component in CFA. However, our findings from the MLPH genotyping did not reveal that the MLPH gene is involved in this skin condition in RRs. However, further genetic studies are needed to clarify the etiology of CFA in RR dogs.

Long-term pedigree analysis: An effective tool for managing congenital malformations in cattle

Controlling congenital defects is an important aspect of breeding for genetic health; however, whether malformations are caused by genetic or nongenetic factors may not be clear. This study aims to analyse the incidence of aplasia genitalis, atresia ani et recti and hernia cerebralis in the Czech cattle population, analyse the relatedness of affected calves by a relationship matrix, and assess the potential future threat. The sires fathering affected calves were born in the Czech Republic or imported from 1986 to 2001. The cases occurred on farms across the Czech Republic. The pedigree of each case was examined for common maternal and paternal ancestors (inbreeding loops) and for ancestors shared by other cases of the defect. The average relatedness coefficient of each individual was computed based on the relationship matrix. The results of the analysis of pedigrees and of the relationship matrix support the hereditary aetiology. The 13 calves affected by aplasia genitalis had common ancestors in 12 cases. The results indicate hereditary causation with recessive inheritance. In atresia ani et recti, some of the pedigrees of 25 affected calves support hereditary causation, and repeating ancestors were found for 11 calves. Our analysis of 11 hernia cerebralis cases also hints at the genetic background, but not as unequivocally as in other congenital defects studied. A high number of descendants fathered by sires of affected calves constitutes a risk for future. The relationship matrix and pedigree analysis could help in managing genetic health, although the final goal in terms of inherited defects must be the description of causal genes and mutations. Measures to control sires and dams with affected calves should be appropriate under the current knowledge, which include culling or prudent use of breeding with the monitoring of descendants.

Consanguineous marriages among Andalusian Gitanos/Calé: a genealogical analysis (1925-2006).

Using data from the family and genealogical reconstitutions of the Gitano population of 22 contiguous localities in eastern Andalusia, Spain, this study analysed the intensity, structure and historical evolution of consanguinity in 3056 couples formed from 1925 to 2006. Of these unions, 54.8% were consanguineous, and 28.7% involved relatives up to and including second cousins, resulting in a mean coefficient of inbreeding up to the third degree α3 = 12.4 × 10-3. The rest of the consanguineous unions (26.1% of all) involved more-distant relatives, such as third cousins, fourth cousins and so forth. When all consanguinity degrees found in the genealogical reconstitution were considered, the total mean coefficient of inbreeding was αt = 14.8 × 10-3. The merging of families and pedigrees generated a complex genealogical network with many inbreeding loops and important founder effects. This network revealed a high rate (62%) of Multiple Consanguineous Marriages (MCMs) in which second and subsequent consanguineous ties increased inbreeding levels by a fifth (20.5%). The accumulation of multiple degrees of distant relatedness, many of which had little social or biological importance, has contributed to a significant increase in inbreeding rates. Among Gitano people, intra-family marriages have remained common in the last decades, in sharp contrast to other Spanish populations. Hence the highest rates of close consanguinity (34%) and inbreeding (α3 = 14.6 × 10-3) were found in the 1960s, the decade that saw the onset of Spain's socioeconomic modernization, internationalization and massive migration. These are among the highest rates of inbreeding found in any European population, including the most endogamous Spanish isolates. They reveal marriage strategies not constrained primarily by geographical barriers, but by ethnocultural separation. Interestingly, in recent decades mixed marriages have been increasing rapidly in this minority, although they are compatible with high rates of consanguinity. Gitano secular endogamy is breaking up, but not uniformly.

Quantifying realized inbreeding in wild and captive animal populations.

Most molecular measures of inbreeding do not measure inbreeding at the scale that is most relevant for understanding inbreeding depression-namely the proportion of the genome that is identical-by-descent (IBD). The inbreeding coefficient FPed obtained from pedigrees is a valuable estimator of IBD, but pedigrees are not always available, and cannot capture inbreeding loops that reach back in time further than the pedigree. We here propose a molecular approach to quantify the realized proportion of the genome that is IBD (propIBD), and we apply this method to a wild and a captive population of zebra finches (Taeniopygia guttata). In each of 948 wild and 1057 captive individuals we analyzed available single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four different genomic regions in each population. This allowed us to determine whether any of these four regions was completely homozygous within an individual, which indicates IBD with high confidence. In the highly nomadic wild population, we did not find a single case of IBD, implying that inbreeding must be extremely rare (propIBD=0-0.00094, 95% CI). In the captive population, a five-generation pedigree strongly underestimated the average amount of realized inbreeding (FPed=0.013<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.

FamSeq: a variant calling program for family-based sequencing data using graphics processing units.

Various algorithms have been developed for variant calling using next-generation sequencing data, and various methods have been applied to reduce the associated false positive and false negative rates. Few variant calling programs, however, utilize the pedigree information when the family-based sequencing data are available. Here, we present a program, FamSeq, which reduces both false positive and false negative rates by incorporating the pedigree information from the Mendelian genetic model into variant calling. To accommodate variations in data complexity, FamSeq consists of four distinct implementations of the Mendelian genetic model: the Bayesian network algorithm, a graphics processing unit version of the Bayesian network algorithm, the Elston-Stewart algorithm and the Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA graphics processing unit. In order to compare the difference in the four methods, we applied FamSeq to pedigree sequencing data with family sizes that varied from 7 to 12. When there is no inbreeding loop in the pedigree, the Elston-Stewart algorithm gives analytical results in a short time. If there are inbreeding loops in the pedigree, we recommend the Bayesian network method, which provides exact answers. To improve the computing speed of the Bayesian network method, we parallelized the computation on a graphics processing unit. This allowed the Bayesian network method to process the whole genome sequencing data of a family of 12 individuals within two days, which was a 10-fold time reduction compared to the time required for this computation on a central processing unit.

Inbreeding Coefficient Estimation with Dense SNP Data: Comparison of Strategies and Application to HapMap III

Background/Aims: If the parents of an individual are related, it is possible for the individual to have received at 1 locus 2 identical-by-descent alleles that are copies of a single allele carried by the parents' common ancestor. The inbreeding coefficient measures the probability of this event and increases with increasing relatedness between the parents. It is traditionally computed from the observed inbreeding loops in the genealogies and its accuracy thus depends on the depth and reliability of the genealogies. With the availability of genome-wide genetic data, it has become possible to compute a genome-based inbreeding coefficient f, and different methods have been developed to estimate f and identify inbred individuals in a sample from the observed patterns of homozygosity at markers. Methods: For this paper, we performed simulations with known genealogies using different SNP panels with different levels of linkage disequilibrium (LD) to compare several estimators of f, including single-point estimates, methods based on the length of runs of homozygosity (ROHs) and different methods that use hidden Markov models (HMMs). We also compared the performances of some of these estimators to identify inbred individuals in a sample using either HMM likelihood ratio tests or an adapted version of the ERSA software. Results: Single-point methods were found to have higher standard deviations than other methods. ROHs gave the best estimates provided the correct length threshold is known. HMMs on sparse data gave equivalent or better results than HMMs modeling LD. Provided LD is correctly accounted for, the inbreeding estimates were very similar using the different SNP panels. The HMM likelihood ratio tests were found to perform better at detecting inbred individuals in a sample than the adapted ERSA. All methods accurately detected inbreeding up to second-cousin offspring. We applied the best method on release 3 of the HapMap phase III project, found up to 4% of inbred individuals, and created HAP1067, an unrelated and outbred dataset of this release. Conclusions: We recommend using HMMs on multiple sparse maps to estimate and detect inbreeding in large samples. If the sample of individuals is too small to estimate allele frequencies, we advise to estimate them on reference panels or to use 1,500-kb ROHs. Finally, we suggest to investigators using HapMap to be careful with inbred individuals, especially in the GIH (Gujarati Indians from Houston in Texas) population.

Fast, exact linkage analysis for categorical traits on arbitrary pedigree designs

Multi-symptom diseases without a consistent continuous measurement of severity may be best understood with a categorical interpretation. In this paper, we present LOCate v.2, a fast, exact algorithm for linkage analysis of all types of categorical traits, both ordinal and nominal. Our method is able to incorporate missing data and analyze complex genealogical structure, including inbreeding loops. LOCate v.2 computes exact likelihoods efficiently through an elimination algorithm, similar to that used by Superlink for binary traits. We compare LOCate v.2 to LOT and QTLlink, two existing methods of linkage analysis for ordinal traits. We find that LOCate v.2 outperforms both methods when used to analyze simulated nominal traits. In addition, LOCate v.2 performs as well as QTLlink on simulated ordinal traits, and better than LOT due to the necessity of cutting large pedigrees for analysis in LOT. To demonstrate the versatility of LOCate v.2, we conduct an ordinal and nominal linkage analysis of ventricular arrhythmias in a large, inbred pedigree of German Shepherd dogs. We find that a trichotomous ordinal or nominal interpretation strengthens the evidence in favor of linkage to a region on chromosome 6, and provides new evidence of linkage to a region on chromosome 11. LOCate v.2 is a unified, fast, and robust method for linkage analysis of ordinal and nominal traits which will be valuable to researchers interested in investigating any type of categorical trait.

A Truncating Mutation in SERPINB6 Is Associated with Autosomal-Recessive Nonsyndromic Sensorineural Hearing Loss

More than 270 million people worldwide have hearing loss that affects normal communication. Although astonishing progress has been made in the identification of more than 50 genes for deafness during the past decade, the majority of deafness genes are yet to be identified. In this study, we mapped a previously unknown autosomal-recessive nonsyndromic sensorineural hearing loss locus (DFNB91) to chromosome 6p25 in a consanguineous Turkish family. The degree of hearing loss was moderate to severe in affected individuals. We subsequently identified a nonsense mutation (p.E245X) in SERPINB6, which is located within the linkage interval for DFNB91 and encodes for an intracellular protease inhibitor. The p.E245X mutation cosegregated in the family as a completely penetrant autosomal-recessive trait and was absent in 300 Turkish controls. The mRNA expression of SERPINB6 was reduced and production of protein was absent in the peripheral leukocytes of homozygotes, suggesting that the hearing loss is due to loss of function of SERPINB6. We also demonstrated that SERPINB6 was expressed primarily in the inner ear hair cells. We propose that SERPINB6 plays an important role in the inner ear in the protection against leakage of lysosomal content during stress and that loss of this protection results in cell death and sensorineural hearing loss.

Genome-wide association study of plasma lipoprotein(a) levels identifies multiple genes on chromosome 6q

Plasma lipoprotein(a) (Lp[a]) level is an independent risk factor of cardiovascular disease that is under strong genetic control. We conducted a genome-wide association study of plasma Lp(a) in 386 members of a founder population that adheres to a communal lifestyle, proscribes cigarette smoking, and prepares and eats meals communally. We identified associations with 77 single nucleotide polymorphisms (SNPs) spanning 12.5 Mb on chromosome 6q26-q27 that met criteria for genome-wide significance (P <or= 1.3 x 10(-7)) and were within or flanking nine genes, including LPA. We show that variation in at least six genes in addition to LPA are significantly associated with Lp(a) levels independent of each other and of the kringle IV repeat polymorphism in the LPA gene. One novel SNP in intron 37 of the LPA gene was also associated with Lp(a) levels and carotid artery disease number in unrelated Caucasians (P = 7.3 x 10(-12) and 0.024, respectively), also independent of kringle IV number. This study suggests a complex genetic architecture of Lp(a) levels that may involve multiple loci on chromosome 6q26-q27.

Platform Highlights Session A 4:30 p.m.-6:00 p.m.

Abstract Samuel F. Berkovic 1,2 , L. M. Dibbens 3 , A. Oshlack 4 , J. D. Silver 4,5 , M. Katerelos 6 , D. F. Vears 1 , J. Stankovich 4,7 , E. Andermann 8 , F. Andermann 8 , B. L. Hodgson 3 , M. A. Bayly 3 , J. C. Mulley 3 , G. K. Smyth 4 , D. A. Power 2,6 and M. Bahlo 4 ( 1 Epilepsy Research Centre and Department of Medicine, University of Melbourne, Heidelberg West, VIC, Australia ; 2 Departments of Neurology and Anatomical Pathology, Austin Health, Heidelberg, VIC, Australia ; 3 Department of Genetic Medicine, Women's and Children's Hospital, Adelaide, SA, Australia ; 4 The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia ; 5 Department of Mathematics and Statistics, University of Melbourne, Parkville, VIC, Australia ; 6 Burnet Institute at Austin, Austin Health, Heidelberg, VIC, Australia ; 7 Menzies Research Institute, University of Tasmania, Hobart, TAS, Australia and 8 Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital McGill University, Montreal, QC, Canada ) Rationale: Action myoclonus renal failure (AMRF) syndrome is a lethal inherited form of progressive myoclonus epilepsy associated with renal failure. It typically presents at 15 – 25 years with neurological symptoms (tremor, action myoclonus, seizures and later ataxia), or proteinuria evolving into renal failure requiring dialysis or transplantation. The autosomal recessive gene defect underlying AMRF was unknown and the lack of large pedigrees and lethality of the disorder precluded a conventional mapping strategy. Methods: We studied three Australian patients and their families: case A of Turkish-Cypriot origin whose parents were first cousins, and cases B and C whose ancestors came from different regions of Britain and no inbreeding loops were known for either family. Using SNP chips and a novel mapping strategy, homozygosity mapping of a known consanguineous case was conducted and then combined with analysis of affected and unaffected siblings in the other families. Results: Homozygosity mapping using all three cases identified a 5.3 cM critical region on chromosome 4 and a second 3.0 cM region on chromosome 20. Microsatellite analysis in these regions excluded the chromosome 20 locus and leaving the chromosome 4 locus as the region of interest. Microarray expression analysis of the two living AMRF patients and their unaffected same sex siblings as controls identified a lysosomal protein as the likely candidate. Sequencing revealed mutations predicted to truncate the protein in all three patients and a subsequent family. Western blotting showed absent expression of this lysosomal membrane protein in lymphocytes. Conclusions: Using only 3 affected individuals, we have identified the gene for this rare form of progressive myoclonus epilepsy. This will allow for earlier diagnosis of this condition and provides new insights into the biology of this disorder. This work was supported by a grant from the Australian National Health and Medical Research Council.

Homozygosity mapping approach identifies a missense mutation in equine cyclophilin B ( PPIB) associated with HERDA in the American Quarter Horse

Hereditary equine regional dermal asthenia (HERDA), a degenerative skin disease that affects the Quarter Horse breed, was localized to ECA1 by homozygosity mapping. Comparative genomics allowed the development of equine gene-specific markers which were used with a set of affected horses to detect a homozygous, identical-by-descent block spanning ∼2.5 Mb, suggesting a recent origin for the HERDA mutation. We report a mutation in cyclophilin B ( PPIB) as a novel, causal candidate gene for HERDA. A c.115G>A missense mutation in PPIB alters a glycine residue that has been conserved across vertebrates. The mutation was homozygous in 64 affected horses and segregates concordant with inbreeding loops apparent in the genealogy of 11 affected horses. Screening of control Quarter Horses indicates a 3.5% carrier frequency. The development of a test that can detect affected horses prior to development of clinical signs and carriers of HERDA will allow Quarter Horse breeders to eliminate this debilitating disease.

Multiple QTLs influencing triglyceride and HDL and total cholesterol levels identified in families with atherogenic dyslipidemia

We conducted a genome-wide scan using variance components linkage analysis to localize quantitative-trait loci (QTLs) influencing triglyceride (TG), high density lipoprotein-cholesterol (HDL-C), low density lipoprotein-cholesterol, and total cholesterol (TC) levels in 3,071 subjects from 459 families with atherogenic dyslipidemia. The most significant evidence for linkage to TG levels was found in a subset of Turkish families at 11q22 [logarithm of the odds ratio (LOD)=3.34] and at 17q12 (LOD=3.44). We performed sequential oligogenic linkage analysis to examine whether multiple QTLs jointly influence TG levels in the Turkish families. These analyses revealed loci at 20q13 that showed strong epistatic effects with 11q22 (conditional LOD=3.15) and at 7q36 that showed strong epistatic effects with 17q12 (conditional LOD=3.21). We also found linkage on the 8p21 region for TG in the entire group of families (LOD=3.08). For HDL-C levels, evidence of linkage was identified on chromosome 15 in the Turkish families (LOD=3.05) and on chromosome 5 in the entire group of families (LOD=2.83). Linkage to QTLs for TC was found at 8p23 in the entire group of families (LOD=4.05) and at 5q13 in a subset of Turkish and Mediterranean families (LOD=3.72). These QTLs provide important clues for the further investigation of genes responsible for these complex lipid phenotypes. These data also indicate that a large proportion of the variance of TG levels in the Turkish population is explained by the interaction of multiple genetic loci.

On the complexity of fundamental computational problems in pedigree analysis.

Pedigree analysis is a central component of many current efforts to locate genes that contribute to diseases or to valuable traits. The analysis usually involves solving one of two very computation-intense problems. We analyze the complexity of these two problems. Surprisingly, we show that both problems are NP-hard even for pedigrees that contain no inbreeding loops.

Linkage Analysis of a Complex Pedigree with Severe Bipolar Disorder, Using a Markov Chain Monte Carlo Method

Recently developed algorithms permit nonparametric linkage analysis of large, complex pedigrees with multiple inbreeding loops. We have used one such algorithm, implemented in the package SimWalk2, to reanalyze previously published genome-screen data from a Costa Rican kindred segregating for severe bipolar disorder. Our results are consistent with previous linkage findings on chromosome 18 and suggest a new locus on chromosome 5 that was not identified using traditional linkage analysis.

The effect of pedigree complexity on quantitative trait linkage analysis.

Due to the computational difficulties of performing linkage analysis on large complex pedigrees, most investigators resort to simplifying such pedigrees by some ad hoc strategy. In this paper, we suggest an analytical method to compare the power of various pedigree simplification schemes by using the asymptotic distribution of the likelihood-ratio statistic. We applied the method to the large Hutterine pedigree. Our results indicate that the breaking and reduction of inbreeding loops can greatly diminish the power to localize quantitative trait loci. We also present an efficient Monte Carlo method for estimating identity-by-descent allele sharing in large complex pedigrees. This method is used to facilitate a linkage analysis of serum IgE levels in the Hutterites without simplifying the pedigree.

Inverse inbreeding coefficient problems with an application to linkage analysis of recessive diseases in inbred populations

Medical geneticists connect relatives having the same disease into a family structure called a pedigree. Genetic linkage analysis uses pedigrees to find the approximate chromosomal locations of disease-causing genes. The problem of choosing a pedigree is particularly interesting for diseases inherited in an autosomal recessive pattern in inbred populations because there are many possible paths of inheritance to choose from. A variety of shortcuts are taken to produce plausible pedigrees from inbred populations. We lay the mathematical foundations for a shortcut that was recently used in a pedigree-disease study of an inbred Mennonite population. Recessive disease genes can be localized using the shortcut of homozygosity mapping by finding regions of the genome where affected persons are homozygous. An important quantity in homozygosity mapping is the inbreeding coefficient of a person, which is the prior probability that the person inherited the same piece of DNA on both copies of the chromosome from a single ancestor. Software packages are ill-suited to handle large pedigrees with many inbreeding loops. Therefore, we consider the problem of generating small pedigrees that match the inbreeding coefficient of one or more affected persons in the larger pedigree. We call such a problem an inverse inbreeding coefficient problem. We focus on the case where there is one sibship with one or more affected persons, and consider the problem of constructing a pedigree so that it is “simpler” and gives the sibship a specified inbreeding coefficient. First, we give a construction that yields small pedigrees for any inbreeding coefficient. Second, we add the constraint that ancestor-descendant matings are not allowed, and we give another more complicated construction to match any inbreeding coefficient. Third, we show some examples of how to use the one-sibship construction to do pedigree replacement on real pedigrees with multiple affected sibships. Fourth, we give a different construction to match the inbreeding coefficient of one sibship, while attempting to minimize a measure of the inbreeding loop complexity.

Linkage mapping of autosomal dominant retinitis pigmentosa (RP1) to the pericentric region of human chromosome 8

Linkage mapping in a large, seven-generation family with type 2 autosomal dominant retinitis pigmentosa (ADRP) demonstrates linkage between the disease locus (RP1) and DNA markers on the short arm of human chromosome 8. Five markers were most informative for mapping ADRP in this family using two-point linkage analysis. The markers, their maximum lod scores, and recombination distances were ANK1 (ankyrin)—2.0 at 16%; D8S5 (TL11)—5.3 at 17%; D8S87 [a(CA) n repeat]—7.2 at 14%; LPL (lipoprotein lipase)—1.5 at 26%; and PLAT (plasminigen activator, tissue)—10.6 at 7%. Multipoint linkage analysis, using a simplified pedigree structure for the family (which contains 192 individuals and two inbreeding loops), gave a maximum lod score of 12.2 for RP1 at a distance 8.1 cM proximal to PLAT in the pericentric region of the chromosome. Based on linkage data from the CEPH (Paris) reference families and physical mapping information from a somatic cell hybrid panel of chromosome 8 fragments, the most likely order for four of these five loci and the diseases locus is 8pter-LPL-D8S5-D8S87-PLAT-RP1. (The precise location of ANK1 relative to PLAT in this map is not established.) The most likely location for RP1 is in the pericentric region of the chromosome. Recently, several families with ADRP with tight linkage to the rhodopsin locus at 3q21–q24 were reported and a number of specific rhodopsin mutations in families with ADRP have since been reported. In other ADRP families, including the one in this study, linkage to rhodopsin has been excluded. Thus mutations at two different loci, at least, have been shown to cause ADRP. There is no remarkable clinical disparity in the expression of disease caused by these different loci.