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PubMed2026

Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights.

Tandem repeat (TR) expansions, including short TRs (motifs ≤6 bp) and variable number TRs (motifs >6 bp), underlie many monogenic disorders, with variable length and sequence influencing pathogenicity, penetrance, severity, and onset. Accurate genotype-phenotype correlation and disease prevalence estimation require characterization beyond repeat length. Here we present a population-scale analysis of 66 disease-associated TR loci using long-read assemblies from 2530 diverse haplotypes from 1265 unaffected donors. Integrating repeat length, motif composition, local ancestry, linkage disequilibrium, and phylogenetic analyses, we reveal extensive locus-, population-, and allele-specific variation shaping disease risk. Up to 8.5% of individuals carry expansions above established pathogenic thresholds, many containing interrupting motifs or sequence structures that attenuate pathogenicity. After excluding alleles from loci with uncertain disease association, non-pathogenic interrupted expansions, and carrier states inconsistent with inheritance patterns, ~4% carried expansions predicted to confer disease risk, largely at adult-onset loci with reduced penetrance. Ancestry-resolved analyses uncover population-specific TR architectures contributing to epidemiological disparities in repeat expansion disorders. Phylogenetic analyses identify conserved ancestral alleles and loci with recent instability. We describe variable linkage disequilibrium patterns and recombination signatures around specific disease-associated TR loci. Our findings emphasize integrating sequence, ancestry, and evolutionary context to understand the complex landscape of disease-associated TRs.

Humans↗
PubMed2006

Novel germline variants identified in the inner mitochondrial membrane transporter TIMM44 and their role in predisposition to oncocytic thyroid carcinomas.

Familial Non-Medullary Thyroid Carcinoma (fNMTC) represents 3-7% of all thyroid tumours and is associated with some of the highest familial risks among all cancers, with an inheritance pattern compatible with an autosomal dominant model with reduced penetrance. We previously mapped a predisposing locus, TCO (Thyroid tumour with Cell Oxyphilia) on chromosome 19p13.2, for a particular form of thyroid tumour characterised by cells with an abnormal proliferation of mitochondria (oxyphilic or oncocytic cells). In the present work, we report the systematic screening of 14 candidate genes mapping to the region of linkage in affected TCO members, that led us to identify two novel variants respectively in exon 9 and exon 13 of TIMM44, a mitochondrial inner membrane translocase for the import in the mitochondria of nuclear-encoded proteins. These variants were co-segregating with the TCO phenotype, were not present in a large group of controls and were predicted to negatively affect the protein (exon 9 change) or the transcript (exon 13 change). Functional analysis was performed in vitro for both changes and although no dramatic loss of function effects were identified for the mutant alleles, subtler effects might still be present that could alter Timm44 function and thus promote oncocytic tumour development. Thus we suggest that TIMM44 should be considered for further studies in independent samples of affected individuals with TCO.

Adenoma, Oxyphilic↗
PubMed2002

Parametric and non-parametric linkage analysis of several candidate regions for genes for human handedness.

The frequency of left-handedness in the general population is around 11%. Both environmental and genetic models have been proposed to explain the aetiology of human handedness. The majority of genetic models, such as those of Annett, McManus and Klar, propose a single gene determinant with a non-Mendelian inheritance pattern. As left-handedness is correlated with cerebral asymmetry and is a feature of left-right asymmetry, genes involved in the development of left-right asymmetry can be considered as candidate genes. Candidate gene analysis was performed using an informative extended pedigree, and also using nuclear families of right-handed parents with left-handed children. Segregation analysis in the extended pedigree identified allele sharing in the NODAL and DNAHC13 candidate regions on chromosome 10 and 1. Linkage analysis using the models of Klar and McManus, and non-parametric analysis on nuclear families, subsequently excluded all candidate regions tested. This demonstrates the power to identify the genes specifying handedness by the conduct of extended genetic studies on these and similar cohorts.

Axonemal Dyneins↗
PubMed2003

Lack of a modulative factor in locus 8p23 in a Finnish family with nonsyndromic sensorineural hearing loss associated with the 1555A>G mitochondrial DNA mutation.

The chromosomal region around marker D8S277 is thought to contribute to susceptibility to hearing impairment in patients with the 1555A>G mutation in mtDNA. We have previously described a family with this mutation, in which some of the members had profound hearing loss, some had a hearing impairment for high-frequency tones and some had completely normal hearing. The phenotypes were thus compatible with a recessive inheritance pattern. We fine-mapped the region around marker D8S277 by sequencing single nucleotide polymorphisms (SNPs) along the 11 Mb region on 8p23, and also sequenced eight defensin genes in the vicinity of D8S277 and the genes GJB2, GJB3, MTO1 and TIMM8A. SNP haplotypes were constructed using the SimWalk2 program. The three persons with a profound hearing loss had identical genotypes in the 11 Mb region on 8p23, but this genotype was also present in a person with normal hearing. The persons with a hearing impairment for high-frequency tones did not share any common haplotype, but one of them shared a genotype with a healthy person. Thus, haplotype comparison excluded a contribution of the region concerned to the expression of hearing impairment in this family, nor could the susceptibility be assigned to the GJB2, GJB3, MTO1 or TIMM8A genes. Extended pedigrees with 1555A>G, such as the present one, provide a good opportunity to identify a modifying nuclear factor. The chromosomal region around 8p23 could be excluded here as the locus for susceptibility to hearing impairment.

Base Sequence↗
PubMed2004

Cosegregation of two unlinked mutant alleles in some cases of autosomal dominant familial exudative vitreoretinopathy.

Familial exudative vitreoretinopathy (FEVR) is a bilateral, clinically and genetically heterogeneous hereditary eye disorder that affects both the retina and the vitreous body. The condition has a high degree of penetrance and variable expressivity. In some cases of autosomal dominant FEVR (AD FEVR), mutations in the frizzled-4 gene (FZD-4) have been shown to be involved in FEVR pathology. In this study, we report that a second unlinked gene (Factor V) is also mutated (Leiden mutation) in the same family, which harbors the FZD-4 gene mutation. These results show for the first time that some families with FEVR could be digenic. While this is unlikely to be a widespread problem, the occurrence of digenic disorders with apparently simple Mendelian inheritance patterns renders the current method of analysis of monogenic disorders by linkage and mutation screening incomplete.

Alleles↗
PubMed2006

Strong linkage on 2q33.3 to familial early-onset generalized osteoarthritis and a consideration of two positional candidate genes.

A genomewide screen was performed in four extended families with early-onset generalized osteoarthritis (FOA) without dysplasia. The FOA phenotype within these families shows a dominant Mendelian inheritance pattern and may represent common osteoarthritis (OA) at later ages. An initial locus was confirmed by three additional families and refined by 14 markers to a two-point logarithm of odds score of 6.05 (theta=0.00) for marker D2S155 at chromosome 2q33.3. This locus coincided with the highest multipoint nonparametric linkage score of 4.70 (P-value=0.0013) at marker D2S2358. Haplotype analysis of family members delineated a narrow region with a number of possible positional candidates, of which we investigate here the two most likely ones: PTHR2, encoding parathyroid hormone receptor 2, and FZD5, encoding frizzled receptor 5. For FZD5, we did not observe a segregating variant, however, for PTHR2, a missense variant (A225S) cosegregated with FOA in one family. The frequency of the PTHR2 variant was rare in a population-based sample, aged 55-70 years (N=1228, 0.4%). Of the 11 carriers, 36% showed generalized radiographic OA as compared to 23% in the remaining population. None of the other families that contributed to the linkage revealed a segregating variant. Together, we have identified a locus on chromosome 2q33.3 for FOA. Candidate gene analysis suggested a possible association of a PTHR2 variant with generalized radiographic OA; it is, however, unlikely the major disease gene for the observed linkage to the FOA phenotype.

Chromosomes, Human, Pair 2↗
PubMed1998

Applications of DNA chips for genomic analysis.

A major frontier in medical genetics is the definition of the molecular basis of multifactorial diseases. This is especially relevant in the field of clinical psychiatry where the majority of common disorders display complex inheritance patterns, and are further influenced by environmental interactions. New technologies are needed to help address the pressing needs for discovering and deciphering the nature of such disease-associated genes. One such technology which has emerged within the past 3 years involves hybridization-based nucleic acid array (DNA chip) analysis. This technology has the potential to have a lasting impact on diverse genomic-based applications such as large-scale gene mapping studies, mutational analysis, and global expression level monitoring of all human genes. In this review we will describe the fundamental principles behind nucleic acid array-based assays, while focusing on their applications towards genome-wide DNA and RNA analysis. The current capabilities and limitations of these technologies will be discussed, with a focus on areas where future development will be needed for DNA chip-based assays to achieve their full potential.

Chromosome Mapping↗
PubMed2003

Sensitivity to sensorimotor gating-disruptive effects of apomorphine in two outbred parental rat strains and their F1 and N2 progeny.

Sensorimotor gating, measured by prepulse inhibition (PPI) of the startle reflex, is reduced in schizophrenia patients and in rats treated with dopamine agonists. Strain and substrain differences in the sensitivity to the PPI-disruptive effects of dopamine agonists may provide insight into the genetic basis for human population differences in sensorimotor gating. We have reported greater sensitivity to the PPI-disruptive effects of the D1/D2 agonist apomorphine in Harlan Sprague-Dawley (SDH) vs Wistar (WH) rats. In the present study, we assessed the inheritance pattern of this phenotypic difference. Sensitivity to the PPI-disruptive effects of apomorphine was compared across parental SDH and WH strains, offspring (F1) of an SDH x WH cross, and subsequent offspring (N2) of an SDH x F1 cross. Apomorphine sensitivity followed a gradient of SDH>N2>F1>WH. Parental SDH and WH strains exhibited comparable sensitivity to the PPI-disruptive effects of phencyclidine. The nature of this gradient of APO sensitivity suggests relatively simple additive effects of multiple genes on the phenotype of PPI sensitivity.

Animals↗
PubMed2004

Clinical genetic study of 144 patients with nonsyndromic hearing loss.

Hearing loss constitutes an important category of congenital defects that can be isolated or part of the phenotypic spectrum of several syndromes. A clinical genetic study was performed on a sample of 144 patients with nonsyndromic hearing loss, establishing the sex distribution, type, degree, symmetry, laterality, progression, etiology, and, when possible, inheritance pattern.

Adolescent↗
PubMed2002

A novel locus (DSAP2) for disseminated superficial actinic porokeratosis maps to chromosome 15q25.1-26.1.

BACKGROUND: Disseminated superficial actinic porokeratosis (DSAP) is a chronic cutaneous disorder characterized by multiple superficial keratotic lesions surrounded by a slightly raised keratotic border. It develops in teenagers in sun-exposed areas of skin and usually follows an autosomal dominant inheritance pattern. The first locus for DSAP was localized to chromosome 12q23.2-24.1, but no gene responsible for porokeratosis has been identified to date. OBJECTIVES: To determine whether DSAP is a genetically heterogeneous disorder and to identify the disease gene locus in a three-generation Chinese family with DSAP. METHODS: Genetic linkage analysis was carried out in this family using 15 microsatellite markers between D12S1671 and D12S369 on chromosome 12q, followed by a genome-wide scan with 382 microsatellite markers from the autosomes. RESULTS: Genetic linkage analysis with chromosome 12q markers suggested that the locus in this family is not linked to chromosome 12q. A genome-wide scan and fine mapping finally localized the locus for DSAP in this family to a 6.4-cM region between markers D15S1023 and D15S1030 at chromosome 15q25.1-26.1. This DSAP locus was named DSAP2. CONCLUSIONS: The previous results and this study have shown that DSAP is a genetically heterogeneous disorder; a novel locus for DSAP, termed DSAP2, was mapped to a 6.4-cM region between markers D15S1023 and D15S1030.

Adolescent↗
PubMed1997

Frequent de novo mutations of the ANK1 gene mimic a recessive mode of transmission in hereditary spherocytosis: three new ANK1 variants: ankyrins Bari, Napoli II and Anzio.

A subset of spherocytosis cases associated with mutations of the ANK1 gene present an apparently recessive inheritance pattern on a clinical and haematological basis. We identified three novel out-of-frame deletions in the ANK1 gene: allele Bari (1361delG), Napoli II (2883delC) and Anzio (3032delCA) in three Italian patients, two of whom have been splenectomized. Analysis of the cDNA showed small or trace amounts of ankyrin mRNAs in Bari, Napoli II and Anzio. The parents were normal clinically and haematologically and did not carry the mutations exhibited by their children. We confirmed the de novo character of the HS mutations based on paternity testing. Recessive HS associated with the ANK1 gene is probably rarer than initially thought, and spherocytosis may often be due to de novo mutations.

Ankyrins↗
PubMed2002

Evaluation of an automated screening assay for von Willebrand disease type 2N.

Evaluating the factor VIII (FVIII) binding activity of von Willebrand factor (VWF) is an important step in the diagnostic work-up of families affected by apparent mild haemophilia A. In von Willebrand's disease (VWD) type 2N (Normandy), mutations at the N-terminal end of the mature VWF subunit gene prevent the binding of FVIII. Individuals heterozygous for type 2N VWD are generally asymptomatic. Homozygotes and compound heterozygotes present with a clinical picture which mimics haemophilia A, with a markedly reduced FVIII : C activity and VWF within the normal range, but instead of exhibiting X-linked inheritance they show an autosomal recessive inheritance pattern. The distinction between haemophilia A and VWD type 2N has important implications for therapy and genetic counselling. We present a highly specific enzyme-linked immunosorbent assay screening method for the Normandy variant, which measures VWF : FVIII binding activity in parallel with VWF antigen, using monoclonal capture and detection antibodies. The assay is fully automated using a robotic microtitre plate processor, requiring minimal user intervention and providing the capacity to screen large numbers of patients.

Automation↗
PubMed1999

An atypical contiguous gene syndrome: molecular studies in a family with X-linked Kallmann's syndrome and X-linked ichthyosis.

BACKGROUND AND OBJECTIVE: Kallmann's syndrome (KS) is characterized by hypogonadotrophic hypogonadism in association with anosmia or hyposmia. This entity can be associated with X-linked ichthyosis (XLI) in a contiguous gene syndrome. Genetic defects have been demonstrated on the Xp22.3 region explaining the presence of one or both entities in affected individuals. In this report we describe the molecular findings in four patients, pertaining to a three generation family, with KS which was associated with XLI in two of them. MEASUREMENTS: Enzymatic activity of steroid sulphatase was measured in leucocytes. Polymerase chain reaction of the 14 exons of the Kallmann gene (KAL) and of the 5' and 3' extremes of the steroid sulphatase gene was performed in genomic DNA. PCR products of the 14 exons of the KAL gene were purified and sequenced. RESULTS: Absence of steroid sulphatase activity and a complete deletion of the STS gene were demonstrated in both patients with XLI. In all subjects, the 14 KAL gene exons amplified in a normal fashion; no mutation was documented after sequencing all exons. CONCLUSIONS: Although it has been proposed recently that the X-linked form of the disease accounts for the minority of patients with Kallman's syndrome, the pedigree chart of this family demonstrates this inheritance pattern. Various possibilities are mentioned in order to explain the absence of mutation in the KAL gene. The coexistence, in this family, of Kallman's syndrome individuals and patients with Kallman's syndrome and X-linked ichthyosis is discussed.

Adult↗
PubMed2003

Linkage and mapping analysis of a non-susceptibility gene to densovirus (nsd-2) in the silkworm, Bombyx mori.

Nonsusceptibility to Bombyx mori densovirus type 2 (BmDNV-2) is controlled by a recessive non-susceptibility gene, nsd-2 (non-susceptibility to DNV-2) in B. mori. Taking advantage of a lack of crossing over in females, reciprocal backcrossed F1 (BF1) progeny were used for linkage analysis and mapping of nsd-2 using silkworm strains C124 and 902, which are classified as being highly susceptible and non-susceptible to DNV-2, respectively. BF1 larvae were inoculated twice with DNV-2 virus at the first and second instar stages. DNA was extracted from each of the surviving fifth instar larvae and analysed by RFLP inheritance patterns using probes specific to each of the 28 linkage groups of B. mori. Our results indicated that the non-susceptibility gene was linked to linkage group 17, since all surviving larvae showed the homozygous profile of strain 902 in their genotype. The other linkage groups showed mixtures of heterozygous and homozygous genotypes, indicating an independent assortment. A linkage map of 30.6 cM was constructed for linkage group 17 with nsd-2 mapped at 24.5 cM and three closely linked cDNA markers were identified.

Animals↗
PubMed2003

ICSI: a technique too far?

Even now 10 years after its introduction, there is still debate on the possible adverse effects of intracytoplasmic sperm injection (ICSI). ICSI has raised a lot of concerns because of the mechanical perforation of the oocyte, the possible transmission of foreign genetic material, the use of immature or senescent germ cells and the association between genetic disorders and some forms of male infertility. To date, the data available indicate that ICSI is a safe procedure provided this treatment is performed in clinics with the highest standards of expertise and with a continuous follow-up programme for the offspring. It is becoming increasingly apparent that it is not ICSI itself, but the background risks of the ICSI patients that represent the major risk factor with regard to congenital malformations. More sex-chromosome abnormalities have been reported in ICSI offspring. Again, the risk of aneuploidy in ICSI progeny reflects the higher aneuploidy rate in the sperm of ICSI fathers. Whether ICSI will eventually perpetuate male infertility is far from clear, because at present the inheritance pattern of idiopathic male infertility is unknown. All ICSI candidates should nevertheless be thoroughly screened and counselled. As long as follow-up studies have a limited power to detect small increases in malformations and as long as no information is available on long-term and next-generation cohorts, ICSI must be used with caution and only when no alternative evidence-based therapy is available. All ICSI candidates should be rigorously screened and thoroughly informed of the limitations of current screening methods and our limited knowledge of the genetic background to male infertility. They should be told that there might be a slight increase in congenital malformation rate after ICSI, but that this increase is probably the result of their own 'background risk'. Well-informed patients are in the best position to judge whether the concerns outweigh the benefits of ICSI.

Congenital Abnormalities↗
PubMed1999

Microsatellite markers and multiple paternity in the garter snake thamnophis sirtalis

Data from four microsatellite loci developed for the common garter snake, Thamnophis sirtalis, show that multiple paternity is common in a natural population on Beaver Island, Michigan. Six of eight litters tested, and all litters with five or more neonates, were multiply sired. At least triple paternity was documented in the largest litter examined (n = 13 neonates). Inheritance patterns and genotype frequencies in the wild population indicate the presence of null allele(s) at one of the microsatellite loci. Garter snakes are widely used in quantitative genetics research, and paternity testing is essential in studies that rely on sibling analysis.

Journal Article↗
PubMed2003

The use of the freer dissector for the removal of trichilemmal cysts.

BACKGROUND: Trichilemmal cysts are keratin-containing cysts, usually situated on the scalp. They often show an autosomal dominant inheritance pattern. Excision is the treatment of choice. We describe a practical surgical technique that eases the removal of these cysts. METHODS: A 24-year-old woman presented with a 5-year history of cystic lesions on her scalp, clinically diagnosed as trichilemmal cysts. She was treated with the new technique. After making a small incision under local anesthesia, a freer dissector (Aesculap(R) OL 165 R) was used as a blunt dissector. The freer dissector was inserted through the incision. A blunt dissection was made to dissect the cyst free from the surrounding dermis and, by using the dissector as a lever, gentle pressure was applied to the opposite side to ease the cyst from the dermis. Four cysts were removed with this technique. RESULTS: The treatment was well tolerated by the patient. No complications developed during or after the procedure. CONCLUSIONS: This modified technique is simple and practical. The slight curve at each end of the freer dissector makes it easy to grasp the cyst and, functioning like forceps, the cyst can be eased from the dermis. We believe that the use of the freer dissector in the surgical excision of trichilemmal cysts aids and speeds up the procedure.

Adult↗
PubMed2003

Genetic testing of the family with a Carney-complex member leads to successful early removal of an asymptomatic atrial myxoma in the mother of the patient.

Carney complex is a rare cardiocutaneous syndrome with an autosomal-dominant inheritance pattern. Apart from its cutaneous manifestations of multiple blue naevi and lentigines, it can involve multiple other organ systems, particularly the heart, where myxoma tumours commonly develop and can potentially lead to serious complications such as cerebrovascular accidents and myocardial infarction. Recently, a specific mutation in the gene encoding the R1-alpha regulatory subunit of cyclic adenosine monophosphate-dependent protein kinase A (PRKAR1alpha) has been discovered and found to be associated with a high risk of developing cardiac myxomas. We report the case of a Carney-complex family member who displayed no observable clinical or cardiac features of the disease but who was found to be positive for the PRKAR1alpha gene mutation on genetic testing. Further evaluation of this patient subsequently led to the discovery of a 3-cm atrial myxoma that had previously been undetected on cardiac assessment. This case highlights the potential benefits of using genetic screening for this disease.

Abnormalities, Multiple↗