Mutations in the gamma-actin gene (ACTG1) are associated with dominant progressive deafness (DFNA20/26)

Age-related hearing loss (presbycusis) is a significant problem in the population. The genetic contribution to age-related hearing loss is estimated to be 40%-50%. Gene mutations that cause nonsyndromic progressive hearing loss with early onset may provide insight into the etiology of presbycusis. We have identified four families segregating an autosomal dominant, progressive, sensorineural hearing loss phenotype that has been linked to chromosome 17q25.3. The critical interval containing the causative gene was narrowed to approximately 2 million bp between markers D17S914 and D17S668. Cochlear-expressed genes were sequenced in affected family members. Sequence analysis of the gamma-actin gene (ACTG1) revealed missense mutations in highly conserved actin domains in all four families. These mutations change amino acids that are conserved in all actins, from protozoa to mammals, and were not found in >100 chromosomes from normal hearing individuals. Much of the specialized ultrastructural organization of the cells in the cochlea is based on the actin cytoskeleton. Many of the mutations known to cause either syndromic or nonsyndromic deafness occur in genes that interact with actin (e.g., the myosins, espin, and harmonin). The mutations we have identified are in various binding domains of actin and are predicted to mildly interfere with bundling, gelation, polymerization, or myosin movement and may cause hearing loss by hindering the repair or stability of cochlear cell structures damaged by noise or aging. This is the first description of a mutation in cytoskeletal, or nonmuscle, actin.

A second kindred linked to DFNA20 (17q25.3) reduces the genetic interval

A family ascertained in the United States displays significant evidence of linkage to 17q25.3 (maximum two-point LOD score 6.32). The non-syndromic autosomal-dominant hearing-loss loci DFNA20 and DFNA26 map to this region. The 3-unit support interval and haplotype for this USA kindred falls within the interval for DFNA20 and DFNA26 and reduces the region to 6.05 cM, according to the deCode genetic map. The same gene is probably responsible for both DFNA20/DFNA26. In addition, the USH1G locus maps to this region and could be an allelic variant of the gene responsible for DFNA20/DFNA26. Clinical data is presented for this kindred, where hearing-impaired family members present with sloping audiograms with mid- and high-frequency hearing loss, which progresses to hearing loss that affects all frequencies. The mean age of onset of hearing impairment is 13.2 years of age (standard deviation: 4.6 years).

Phenotypes and genetic analysis of psychiatric and neuropsychiatric traits

A workshop was held at Rockefeller University entitled "Phenotypes and Genetic Analysis of Complex Traits." The purpose of the workshop was to examine phenotype definition for complex traits, in particular, psychiatric and neuropsychiatric traits. An additional goal of the workshop was to examine statistical genetic approaches that specifically address the oligogenic nature of psychiatric traits. An overview of topics that were addressed and discussed at the workshop is presented in this article.

Novel selection criteria for genome scans of complex traits

Due to their oligogenic inheritance, the identification of susceptibility loci for complex traits by classical selection criteria has not been very successful. One way to address this problem is to identify statistics that measure the effect of more than one locus simultaneously. In the approach described here, a p-value is assigned to a combination of loci under the null hypothesis that none of them is linked to the disease locus. In order to examine the power of this method to detect multiple loci, the Genetic Analysis Workshop 12 general population simulated data set was analyzed using variance component methods. Using the described novel selection criteria resulted in an increase of power, however, a rejection of the null hypothesis has to be interpreted with care.

Mapping of a gene for severe pediatric gastroesophageal reflux to chromosome 13q14

CONTEXT

Gastroesophageal reflux (GER) has not previously been widely regarded as a hereditary disease. A few reports have suggested, however, that a genetic component may contribute to the incidence of GER, especially in its severe or chronic forms.

OBJECTIVE

To identify a genetic locus that cosegregates with a severe pediatric GER phenotype in families with multiple affected members.

DESIGN

A genome-wide scan of families affected by severe pediatric GER using polymorphic microsatellite markers spaced at an average of 8 centimorgans (cM), followed by haplotyping and by pairwise and multipoint linkage analyses.

SETTING

General US community, with research performed in a university tertiary care hospital.

SUBJECTS

Affected and unaffected family members from 5 families having multiple individuals affected by severe pediatric GER, identified through a patient support group.

MAIN OUTCOME MEASURES

Determination of inheritance patterns and linkage of a genetic locus with the severe pediatric GER phenotype by logarithm-of-odds (lod) score analysis, considering a lod score of 3 or greater as evidence of linkage.

RESULTS

In these families, severe pediatric GER followed an autosomal dominant hereditary pattern with high penetrance. A gene for severe pediatric GER was mapped to a 13-cM region on chromosome 13q between microsatellite markers D13S171 and D13S263. A maximum multifamily 2-point lod score of 5.58 and a maximum multifamily multipoint lod score of 7.15 were obtained for marker D13S1253 at map position 35 cM when presumptively affected persons were modeled as unknown (a maximum multipoint score of 4.88 was obtained when presumptively affected persons were modeled as unaffected).

CONCLUSION

These data suggest that a gene for severe pediatric GER maps to chromosome 13q14. JAMA. 2000;284:325-334

The ascertainment of multiplex schizophrenia pedigrees from Daghestan genetic isolates (Northern Caucasus, Russia)

This article describes the preliminary ascertainment of multiplex schizophrenia pedigrees from the isolated mountain region of Daghestan (Northern Caucasus, Russia). Daghestan has a population of two million people and contains 26 aboriginal ethnic groups. Many of the ethnic groups reside in remote mountain villages that can be classified as 'primary isolates'. Prolonged reproductive isolation and severe environmental conditions in the highlands have created diverse, genetically isolated ethnic populations in Daghestan. A number of the isolates in this region contain large extended multiplex schizophrenia pedigrees that are ideal for genetic analyses. During summer expeditions of 1996 and 1997, 14 separate large multiplex schizophrenia pedigrees were ascertained from 14 different mountain villages. Of the 14 kindreds, one had 50 schizophrenic cases available for ascertainment, one had 32, and another had 24. Seven of the remaining pedigrees had between 11 and 23 living cases. Within the kindreds, the number of males with chronic schizophrenia was at least twice that of females. The average age of onset of schizophrenia is 21.2 years for offspring of consanguineous marriages and 17.4 years for offspring of nonconsanguineous marriages (P = 0.033). Although the pedigrees ascertained from the remote mountain villages may not be representative of the general population, they are unique kindreds for mapping schizophrenia susceptibility genes.

A novel locus (DFNA23) for prelingual autosomal dominant nonsyndromic hearing loss maps to 14q21-q22 in a Swiss German kindred

DFNA23, a novel locus for autosomal dominant nonsyndromic hearing loss, was identified in a Swiss German kindred. DNA samples were obtained from 22 family members in three generations: 10 with hearing impairment caused by the DFNA23 locus, 8 unaffected offspring, and 4 spouses of hearing-impaired pedigree members. In this kindred, the hearing-impaired family members have prelingual bilateral symmetrical hearing loss. All audiograms from hearing-impaired individuals displayed sloping curves, with hearing ability ranging from normal hearing to mild hearing loss in low frequencies, normal hearing to profound hearing loss in mid frequencies, and moderate to profound hearing loss in high frequencies. A conductive component existed for 50% of the hearing-impaired family members. The majority of the hearing-impaired family members did not display progression of hearing loss. The DFNA23 locus maps to 14q21-q22. Linkage analysis was carried out under a fully penetrant autosomal dominant mode of inheritance with no phenocopies. A maximum multipoint LOD score of 5.1 occurred at Marker D14S290. The 3.0-LOD unit support interval is 9.4 cM and ranged from marker D14S980 to marker D14S1046.

Effects of stratification in the analysis of affected-sib-pair data: benefits and costs

The benefits and costs of stratification of affected-sib-pair (ASP) data were examined in three situations: (1) when there is no difference in identity-by-descent (IBD) allele sharing between stratified and unstratified ASP data sets; (2) when there is an increase in IBD allele sharing in one of the stratified groups; and (3) when the data are stratified on the basis of IBD allele-sharing status at one locus, and the stratified ASPs are then analyzed for linkage at a second locus. When there is no difference in IBD sharing between strata, a penalty is always paid for stratifying the data. The loss of power to detect linkage in the stratified ASP data sets is the result of multiple testing and the smaller sample size within individual strata. In the case in which etiologic heterogeneity (i.e., severity of phenotype, age at onset) represents genetic heterogeneity, the power to detect linkage can be increased by stratifying the ASP data. This benefit is obtained when there is sufficient IBD allele sharing and sample sizes. Once linkage has been established for a given locus, data can be stratified on the basis of IBD status at this locus and can be tested for linkage at a second locus. When the relative risk is in the vicinity of 1, the power to detect linkage at the second locus is always greater for the unstratified ASP data set. Even for values of the relative risk that diverge sufficiently from 1, with adequate sample sizes and IBD allele sharing, the benefits of stratifying ASP data are minimal.

An analytic solution to single nucleotide polymorphism error-detection rates in nuclear families: implications for study design

Recently, there has been increased interest in using Single Nucleotide Polymorphisms (SNPs) as a method for detecting genes for complex traits. SNPs are diallelic markers that have the potential to be inexpensively produced using chip technology. It has been suggested that SNPs will be beneficial in study designs that utilize trio data (father, mother, child). In our previous work, we calculated the probability of detecting Mendelian errors at a SNP locus for a trio randomly selected from a population in Hardy-Weinberg equilibrium. The highest error-detection rate was 30%. Here we investigate the error-detection rate when additional sibs are genotyped. We define an error to be a change from a 1 allele to a 2 allele, or vice versa. Typing one additional sib increases the detection rate on average by 10-13%. Typing two additional sibs increases the detection rate on average by 14-19%. The increase in the detection rate is dependent on the allele frequencies. Equal allele frequencies produce the lowest detection rates, independent of true error rates and number of offspring genotyped. Typing additional siblings not only improves error-detection rates, but can also provide additional linkage information. In order to increase linkage information and error-detection rates, at least two additional siblings should be ascertained when available.

Double outlet right ventricle with anterior and left-sided aorta and subpulmonary ventricular septal defect

Double outlet right ventricle (DORV) is a heterogeneous group of abnormal ventriculoarterial connections where, by definition, both great arteries (pulmonary artery and aorta) arise primarily from the morphologically right ventricle. This condition affects 1-1.5% of the patients with congenital heart diseases, with a frequency of 1 in each 10,000 live births. We report the case of an 18-day-old infant with DORV and extremely rare anatomical features, such as anterior and left-sided aorta and subpulmonary ventricular septal defect (VSD). In addition to the anatomic features, the role of the echocardiogram for guiding the diagnosis and the surgical therapy of this congenital heart disease are discussed.

Genetic and physiologic analysis of the role of uncoupling protein 3 in human energy homeostasis

By virtue of its potential effects on rates of energy expenditure, uncoupling protein 3 (UCP3) is an obesity candidate gene. We identified nine sequence variants in UCP3, including Val9Met, Val102Ile, Arg282Cys, and a splice site mutation in the intron between exons 6 and 7. The splice mutation results in an inability to synthesize mRNA for the long isoform (UCP3L) of UCP3. Linkage (sib pair), association, and transmission disequilibrium testing studies on 942 African-Americans did not suggest a significant effect of UCP3 on body composition in this group. In vastus lateralis skeletal muscle of individuals homozygous for the splice mutation, no UCP3L mRNA was detectable; the short isoform (UCP3S) was present in an increased amount. In this muscle, we detected no alterations of in vitro mitochondrial coupling activity, mitochondrial respiratory enzyme activity, or systemic oxygen consumption or respiratory quotient at rest or during exercise. These genetic and physiologic data suggest the following possibilities: UCP3S has uncoupling capabilities equivalent to UCP3L; other UCPs may compensate for a deficiency of bioactive UCP3L; UCP3L does not function primarily as a mitochondrial uncoupling protein.

Homozygosity mapping of the Achromatopsia locus in the Pingelapese

Achromatopsia, or total color blindness (also referred to as "rod monochromacy"), is a severe retinal disorder characterized clinically by an inability to distinguish colors, impaired visual acuity in daylight, photophobia, and nystagmus. Inherited as an autosomal recessive trait, achromatopsia is rare in the general population (1:20,000-1:50,000). Among the Pingelapese people of the Eastern Caroline Islands, however, the disorder occurs at an extremely high frequency, as recounted in Oliver Sacks's popular book The Island of the Colorblind: 4%-10% of this island population have the disorder and approximately 30% carry the gene. This extraordinary enrichment of the disease allele most likely resulted from a sharp reduction in population in the late 18th century, in the aftermath of a typhoon and subsequent geographic and cultural isolation. To obtain insights into the genetic basis of achromatopsia, as well as into the genetic history of this region of Micronesia, a genomewide search for linkage was performed in three Pingelapese kindreds with achromatopsia. A two-step search was used with a DNA pooling strategy, followed by genotyping of individual family members. Genetic markers that displayed a shift toward homozygosity in the affected DNA pool were used to genotype individual members of the kindreds, and an achromatopsia locus was identified on 8q21-q22. A maximal multipoint LOD score of 9.5 was observed with marker D8S1707. Homozygosity was seen for three adjacent markers (D8S275, D8S1119, and D8S1707), whereas recombination was observed with the flanking markers D8S1757 and D8S270, defining the outer boundaries of the disease-gene locus that spans a distance of <6.5cM.

The long isoform uncoupling protein-3 (UCP3L) in human energy homeostasis

The biological role(s) proposed for UCP3 in energy homeostasis have been based primarily upon amino acid sequence homology to UCP1. Spontaneous mutations of UCP3> have been described in humans, but not in rodents. The functional consequences-or lack thereof-of these mutations in humans will be of great importance in elucidating the biology of this protein. The results of two such studies are summarized here.

Interactions of high affinity insulin-like growth factor-binding proteins with the type V transforming growth factor-beta receptor in mink lung epithelial cells

High affinity insulin-like growth factor-binding proteins (IGFBP-1 to -6) are a family of structurally homologous proteins that induce cellular responses by insulin-like growth factor (IGF)-dependent and -independent mechanisms. The IGFBP-3 receptor, which mediates the IGF-independent growth inhibitory response, has recently been identified as the type V transforming growth factor-beta receptor (TbetaR-V) (Leal, S. M., Liu, Q. L., Huang, S. S., and Huang, J. S. (1997) J. Biol. Chem. 272, 20572-20576). To characterize the interactions of high affinity IGFBPs with TbetaR-V, mink lung epithelial cells (Mv1Lu cells) were incubated with 125I-labeled recombinant human IGFBPs (125I-IGFBP-1 to -6) in the presence of the cross-linking agent disuccinimidyl suberate and analyzed by 5% SDS-polyacrylamide gel electrophoresis and autoradiography. 125I-IGFBP-3, -4, and -5 but not 125I-IGFBP-1, -2, and -6 bound to TbetaR-V as demonstrated by the detection of the approximately 400-kDa 125I-IGFBP.TbetaR-V cross-linked complex in the cell lysates and immunoprecipitates. The analyses of 125I-labeled ligand binding competition and DNA synthesis inhibition revealed that IGFBP-3 was a more potent ligand for TbetaR-V than IGFBP-4 or -5. Most of the high affinity 125I-IGFBPs formed dimers at the cell surface. The cell-surface dimer of 125I-IGFBP-3 preferentially bound to and was cross-linked to TbetaR-V in the presence of disuccinimidyl suberate. IGFBP-3 did not stimulate the cellular phosphorylation of Smad2 and Smad3, key transducers of the transforming growth factor-beta type I/type II receptor (TbetaR-I.TbetaR-II) heterocomplex-mediated signaling. These results suggest that IGFBP-3, -4, and -5 are specific ligands for TbetaR-V, which mediates the growth inhibitory response through a signaling pathway(s) distinct from that mediated by the TbetaR-I and TbetaR-II heterocomplex.

Fine mapping of progressive pseudorheumatoid dysplasia: a tool for heterozygote identification

Progressive pseudorheumatoid dysplasia is a skeletal genetic disorder affecting primarily the articular cartilage, causing joint stiffness and leading to a crippling status. More than two-thirds of the reported patients belong to Arab and Mediterranean populations. The disease locus has been mapped to chromosome 6q22 in a region of 12.9 cM using a Jordanian family. We examined two additional families, one Jordanian and one Palestinian, to test for homogeneity of the disorder and the presence of a common haplotype, to fine map the disorder, and to use all the information to derive a tool for heterozygote identification. The two families showed linkage to the same previously reported locus, thus suggesting homogeneity, but they did not share a common haplotype. They also provided information that refined the genetic region for the disease locus to 2.1 cM with three microsatellite markers. The absence of a common haplotype indicates that no common ancestor mutations were inherited by our patients. Genotyping for the three-marker haplotype showed that it can be used as a heterozygote identification tool.

Searching for alcoholism susceptibility genes using Markov chain Monte Carlo methods

Markov chain Monte Carlo (MCMC) methods offer a rapid parametric approach that can test for linkage throughout the entire genome. It has an advantage similar to nonparametric methods in that the model does not have to be completely specified a priori. However, unlike nonparametric methods, there are no limitations on pedigree size and MCMC methods can also handle relatively complex pedigree structures. In addition MCMC methods can be used to carry segregation analysis in order to answer questions on the genetic components of a disease phenotype. Segregation analysis gave evidence for between two and eight alcoholism susceptibility loci, each having a modest effect on the phenotype. MCMC methods were used to map alcoholism loci using the phenotypes ALDX1 (DSM-III-R and Feighner criteria) and ALDX2 (World Health Organization diagnosis ICD-10 criteria). There was mild evidence for quantitative trait loci on chromosomes 2, 10, and 11.

[Hereditary deafness in Turkey. Initial results]

The authors describe a study in progress to identify Turkish families with hereditary hearing loss and isolate possible responsible disease genes. Due to extreme genetic heterogeneity and limited audiological differentiation of hereditary hearing loss, it is necessary to identify large or small families from genetic isolates to locate loci responsible for hearing loss on a chromosome. To accomplish this goal, the medical records of 3800 children were examined at the ENT Clinic of Ege University between 1975 and 1994. All were suspected of having various hearing impairments. Additionally, students from two schools for the hearing impaired in Izmir and Eskisehir, Turkey were examined. To date, 16 families with syndromal deafness and 55 families with non-syndromal hereditary hearing loss involving two or more affected individuals have been identified and categorized according to the mode of inheritance. The majority (66%) of the non-syndromal families showed an autosomal recessive pattern, 29% an autosomal dominant inheritance and 5% an X-linked mode of inheritance. In the study presented there has been a predominance of affected males versus females and the consanguinity rate was 22%.

Single-nucleotide polymorphism in the human mu opioid receptor gene alters beta-endorphin binding and activity: possible implications for opiate addiction

Opioid drugs play important roles in the clinical management of pain, as well as in the development and treatment of drug abuse. The mu opioid receptor is the primary site of action for the most commonly used opioids, including morphine, heroin, fentanyl, and methadone. By sequencing DNA from 113 former heroin addicts in methadone maintenance and 39 individuals with no history of drug or alcohol abuse or dependence, we have identified five different single-nucleotide polymorphisms (SNPs) in the coding region of the mu opioid receptor gene. The most prevalent SNP is a nucleotide substitution at position 118 (A118G), predicting an amino acid change at a putative N-glycosylation site. This SNP displays an allelic frequency of approximately 10% in our study population. Significant differences in allele distribution were observed among ethnic groups studied. The variant receptor resulting from the A118G SNP did not show altered binding affinities for most opioid peptides and alkaloids tested. However, the A118G variant receptor binds beta-endorphin, an endogenous opioid that activates the mu opioid receptor, approximately three times more tightly than the most common allelic form of the receptor. Furthermore, beta-endorphin is approximately three times more potent at the A118G variant receptor than at the most common allelic form in agonist-induced activation of G protein-coupled potassium channels. These results show that SNPs in the mu opioid receptor gene can alter binding and signal transduction in the resulting receptor and may have implications for normal physiology, therapeutics, and vulnerability to develop or protection from diverse diseases including the addictive diseases.

Dobutamine stress echocardiography in anomalous left coronary artery

The evaluation of left ventricular function with dobutamine stress echocardiography is described for the first time in a patient with anomalous left coronary artery from the pulmonary trunk during the preoperative and postoperative periods. This method demonstrated signs of myocardial ischemia that were not seen on the resting echocardiogram during the preoperative period and ventricular function recovery after surgical intervention.

A second middle eastern kindred with autosomal recessive non-syndromic hearing loss segregates DFNB9

A second kindred has been identified which supports the previously reported location of DFNB9. Linkage has been established to markers closely linked to DFNB9 which is located on 2p22-p23. The hearing impaired individuals in this highly consanguineous kindred from Eastern Turkey have prelingual profound hearing loss which affects all frequencies. A genetic map of the 2p22-p23 region where DFNB9 resides was generated using marker genotypes available from the CEPH database. All markers were placed on this genetic map using a likelihood ratio criterion of 1000:1. This map suggests that the region for DFNB9 is less than 1.08 cM, 95% confidence interval (0-2.59 cM).

The type V transforming growth factor beta receptor is the putative insulin-like growth factor-binding protein 3 receptor

Insulin-like growth factor-binding protein 3 (IGFBP-3) has been shown to inhibit cell growth by IGF-dependent and -independent mechanisms. The putative cell-surface IGFBP-3 receptor that mediates the IGF-independent growth inhibition has not been identified. Here we show that recombinant human IGFBP-3 inhibits 125I-transforming growth factor (TGF)-beta1 binding to the type V TGF-beta receptor (Mr 400,000) in mink lung epithelial cells. We also demonstrate that the approximately 400-kDa 125I-IGFBP-3 affinity-labeled putative IGFBP-3 receptor is immunoprecipitated by specific antiserum to the type V TGF-beta receptor. The 125I-IGFBP-3 affinity labeling of the putative receptor and IGFBP-3-induced growth inhibition as measured by DNA synthesis in these cells is blocked by a TGF-beta1 peptide antagonist. The 125I-IGFBP-3 affinity-labeled putative receptor can only be detected in cells expressing the type V TGF-beta receptor, but not in cells lacking the type V TGF-beta receptor. These results indicate that the type V TGF-beta receptor is the putative IGFBP-3 receptor and that IGFBP-3 is a functional ligand for the type V TGF-beta receptor.

Is there a genetic susceptibility locus for Parkinson's disease on chromosome 22q13?

The cytochrome P450 mono-oxygenase gene, CYP2D6 on chromosome 22q13 (ch22q13), has been inconsistently associated with Parkinson's disease. Associations with CYP2D6 have either been absent altogether or have involved more than one polymorphism, many of which have the same metabolic effect on gene expression. We examined the association between CYP2D6 polymorphisms and Parkinson's disease in a case-control study and included 10 polymorphic dinucleotide repeat markers linked to CYP2D6 to determine whether the association was present or due to linkage disequilibrium. There was no association between any polymorphism of CYP2D6 and Parkinson's disease, but two of 10 dinucleotide repeat markers linked to CYP2D6 were associated with the disease. These results provide evidence to suggest that there may be an unidentified locus for susceptibility to Parkinson's disease that is in linkage disequilibrium with dinucleotide repeat markers mapping near CYP2D6 on ch22q13.

False positive rates in a genomic screen for complex quantitative traits

We conducted a genomic screen for genes associated with Q1, Q2, and Q3 in 239 nuclear pedigrees from replicate 115, Problem Set 2A. We compared false positive (FP) and true positive (TP) rates for three significance levels and two map densities. Using the 2 cM genetic map and alpha = 0.05 produced the most FP but detected the greatest number of major genes. Following up only 31 plateaus (two or more adjacent markers with significant results) from the 2 cM screen eliminated some FP, but failed to detect MG3 for Q3. Multipoint analysis reduced the number of priority regions from 31 to seven; only two of these regions were TP. Replication of the two-point analysis of plateau markers in replicate 80 detected all of the genes associated with Q1 and Q2, but not Q3. Multipoint analysis in replicate 80 failed to replicate any genes associated with Q1, Q2, or Q3, but "replicated" two FP regions. While FP may be reduced by decreasing map density, considering only plateaus for follow up and decreasing significance levels, such adjustments may also fail to detect weak TP. Multipoint analysis and replication in independent data sets may not be reliable methods of distinguishing FP from TP.