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Genetic epidemiology of early onset breast cancer.

Risks for breast cancer when there is a family history of the disease are usually calculated using data from segregation analyses which favour a single dominant gene with high penetrance. There are, however, at least three loci known to be associated with familial breast cancer (p53, BRCA1, and an as yet unpublished locus) and the frequencies and penetrances of these genes are not likely to be the same. We have attempted to address the problem of which genetic parameters should be used to calculate risks for different patterns of familial breast cancer. Data from 384 nuclear families ascertained through a proband selected for early onset breast cancer were subjected to complex segregation analysis, correcting for ascertainment bias resulting from selection for severe phenotype. Age of onset of breast cancer, incorporated as severity, provides additional information to the segregation model over and above that given by assigning liability classes on the basis of age at observation. The use of this additional parameter in the analysis is described. There is fair agreement between estimates from this sample and previous predictions from consecutive probands and consultands. The differences suggest more than one rare dominant gene for susceptibility to breast cancer, with different penetrances. Although refinements of segregation analysis will help to delineate these different genes, perfect resolution will require identification of the mutant alleles. Methods to estimate genetic parameters under genotype specific mortality need to be developed. Meanwhile, we suggest that high and low estimates of penetrance be used in risk estimation for genetic counselling, and as a guide to candidates for entry into clinical trials of screening and chemoprevention in breast cancer.

Adult↗

Genetic profile of 81 retinoblastoma patients from a referral hospital in southern India.

PURPOSE: To determine chromosomal abnormalities and inheritance pattern in patients with retinoblastoma from a referral hospital in southern India. MATERIALS AND METHODS: Eighty-one retinoblastoma patients from 78 families were included in this study. Peripheral venous blood was taken for chromosomal analysis and pedigree was ascertained for segregation analysis. RESULTS: Male to female ratio was 1.7:1, 55.56% were bilateral retinoblastoma, the mean age of onset was 12.37 months in bilateral and 33.07 months in unilateral cases (p=0.048). Majority (90.12%) had sporadic inheritance and 6.17% had autosomal dominant inheritance. In chromosomal abnormalities, 8.33% had 13q14 deletion, three cases had de novo balanced translocations. CONCLUSION: The age of onset of the disease was much earlier in the bilateral cases compared to unilateral cases. Sporadic inheritance was predominant while only a small percentage of patients had autosomal dominant inheritance. The percentage of patients with 13q14 deletion was higher than reported in the literature and three novel chromosomal translocations were observed. This is one of the largest series of cases reported from India.

Adolescent↗

Combined association, segregation and aggregation analysis on case-control family data.

Recently genetic epidemiologists have begun using case-control family study designs to investigate the role of genetic and environmental risk factors in disease etiology. The objective of these studies is to assess the association of environmental factors with the disease trait; to characterize the disease genes using segregation analysis; and to quantify the residual familial aggregation after controlling for environmental and genetic factors. Typically these objectives are achieved by conducting separate studies and analysis. This paper describes an estimating equation based approach for a combined association, segregation and aggregation analysis on data from case-control family studies. Simulations indicate that the method performs well in a variety of settings. The method is illustrated using simulated family history data made available to participants in a recent Genetic Analysis Workshop.

Journal Article↗

Multidirectional interactions in vitro between lymphoid cells from Mls-disparate strains.

Chromosome 1 of the mouse carries a number of genes for alloantigens which can be recognized by T cells, among those the mixed lymphocyte stimulation (Mls) locus and the lymphocyte stimulating determinant (Lsd) locus have been described. The Relationship between the antigens coded for by these two loci has been further analyzed using a B10.BR anti C3H/Tif T cell clone E11. Segregation analysis was done with 167 individuals from backcrosses of (BALB/c (Mlsb, Lsd-) x DBA/2 (Mlsa, Lsd+] F1 animals into BALB/c mice. The analysis of the backcross data and of a limited number of recombinant inbred (RI) strains did not allow the segregated of the two loci, despite the fact that stable clusters were obtained in cluster analysis of the segregation data. The reasons for this failure are discussed. Parallel to the genetic analysis, we have studied the functional properties of the E11 T cell clone. First, there is the proliferation of the E11 T cells upon stimulation by macrophages or B cells of Mls-disparate stimulator strains. Second, there is an induction of differentiation of B cells of stimulator strains, requiring the direct interaction between E11 T and stimulator B cells. Third, there is an inhibitory influence of E11 T cells on the production of a mediator by Mls-disparate spleen cells presumably by their macrophages. We propose that the Mls antigen is a receptor regulating macrophage differentiation and transmitting a signal influencing the production of a mediator. This signal could be either the down regulation of the production of a stimulatory monokine or the induction of the production of an inhibitory monokine. Our presented data demonstrate that the anti Mls response is more complex than hitherto anticipated. It involves a multidirectional interaction between the Mls-disparate cell partners.

Animals↗

Segregation and linkage analyses of dopamine-beta-hydroxylase activity in a six-generation pedigree.

Serum dopamine-beta-hydroxylase (DBH) levels and 30 polymorphic markers were determined on 178 individuals of the HGAR 29 family, ascertained through six probands who had clinical and electrocardiographic evidence of myocardial infarction. Individuals in this pedigree with a history of heart attack had significantly lower levels of DBH, but this difference was partly confounded with age differences. Pedigree segregation analysis showed evidence of a codominant gene for DBH segregating in the family. Linkage analysis between the putative DBH locus and 30 polymorphic marker loci, assuming a codominant model, yielded a largest lod score of 0.53, with ABO at 20% recombination. Adding this to the lod scores obtained by Elston et al [1979] and Goldin et al [1982], we obtain combined lod scores of 2.49 and 2.50 at 0.0 and 10% recombination respectively.

ABO Blood-Group System↗

Restriction fragment length polymorphism analysis of HLA haplotypes in families with type I diabetes mellitus.

HLA Class II polymorphisms were analysed in 27 families with at least one Type I diabetic proband using Southern blotting technique according to 10th Histocompatibility Workshop Standards. The probes used were DRB, DQA1, DQB1 and DOB. We have studied 108 haplotypes and performed segregation analysis with HLA serology and restriction fragment length polymorphism (RFLP) data and compared "affected" with "non-affected" haplotypes (not inherited by IDDM patients). RFLPs correlated well with DR and DQ serology and detected additional polymorphisms. In particular, DQB polymorphism analysis showed segregation of the DQw3 splits with 88.5% of the DR4 affected haplotypes bearing the DQw3.2 split (now DQw8) and 11.5% the DQw3.1 split (now DQw7) while in the non-affected DR4 haplotypes 33.3% were DQw3.2 and 66.6% were DQw3.1. Haplotype analysis showed that DR4-DQw3.2 was in strong linkage with the U fragment (2.1 kb Taq I) of DQA2 (DX alpha) and with the L fragment (5.4 kb BamH I) of DOB. This study confirms previous observations of DQB polymorphisms in heterozygous IDDM patients, supports the protective effect of DQw3.1 (DQw7) against the development of the disease and demonstrates the importance of DQw3.2 (DQw8) for susceptibility to Type I diabetes.

Diabetes Mellitus, Type 1↗

Gonadal (ovarian) dysgenesis in 46,XX individuals: frequency of the autosomal recessive form.

Gonadal (ovarian) dysgenesis with normal chromosomes (46,XX) clearly is a heterogeneous condition. In some forms, the defect is restricted to the gonads, whereas other affected females show neurosensory hearing loss (Perrault syndrome). In another form, brothers may have germ cell aplasia [Granat et al., Fertil Steril 1983; 40:215-219]. Nongenetic causes exist as well. To elucidate the proportion of XX gonadal (ovarian) dysgenesis due to autosomal recessive genes, we analyzed published (N = 17) and unpublished (N = 8) families having at least two female offspring. Analysis was restricted to cases in whom ovarian failure was documented by the presence of streak ovaries (published cases) or elevated gonadotropins (unpublished cases). We reasoned that the closer to that segregation ratio expected for an autosomal recessive trait (0.25), the lower the frequency of nongenetic forms. Segregation analysis utilized standard correction for single ascertainment, with only females included in the preliminary analysis. The segregation ratio estimate was 0.16. Our results suggest that many 46,XX females with gonadal (ovarian) dysgenesis represent a disorder segregating as an autosomal recessive trait, placing sisters of these cases at a 25% risk for this disorder.

Female↗

A genetic study of hypoalphalipoproteinemia.

Complex segregation analysis under the unified mixed model of inheritance (major gene and multifactorial) is performed on families ascertained through 23 probands with hypoalphalipoproteinemia (depressed HDL-cholesterol, denoted HDL-c). Evidence for segregation of a recessive major gene for depressed HDL-c with frequency q = 0.116, in addition to multifactorial transmission (H = 0.572), is found in these families. Reanalysis of a subset of families with severely depressed HDL-c confirms the conclusions based on the original analysis, except that different definitions of "affection" give rise to different estimates of gene frequency. Our finding of a recessive mode of inheritance differs from previous claims for a dominant gene because previous analyses did not use a mixed model for segregation analysis of hypoalphalipoproteinemia. When the significant multifactorial background is neglected, we also find evidence for the invalid claim of a dominant gene. This demonstrates the necessity of using mixed models for determining the mode of inheritance of a given phenotype.

Cholesterol, HDL↗

Yield and yield component trait analysis with DArT genotyping for GWAS in soybean grown in drought conditions of Kazakhstan.

Development of drought tolerant cultivars of soybean is the single best way to address the challenge of global climate change and very limited water resources for crop irrigation in Central Asia including Kazakhstan. A set of 188 soybean cultivars with diverse origins was assessed for genome-wide association study (GWAS) for yield and eight yield-related traits in both irrigated (well-watered, WW) and non-irrigated (drought) conditions during 2 years in field trials in South-Eastern Kazakhstan. The 295K Diversity array technology (DArT) analysis was applied, and 16K filtered DArT markers were used for genotyping of 183 soybean accessions. In the results, 41 quantitative trait nucleotides (QTN) were identified as significantly associated with nine studied traits. To verify these results, bulk segregant analysis (BSA) was carried out in six breeding lines originating from two crosses between high-yielding under drought cvs, Sponsor and Zen, with drought sensitive cv Lastochka. The evaluation of combined results revealed 10 most significant QTN and eight most promising putative candidate genes, which were selected and tested for their gene expression using RT-qPCR under drought compared with WW controls. Among them, glucose-6-phosphate isomerase (G6PI), pentatricopeptide repeats (PPR) protein, and ABC transporter, associated with seed yield, seed weight per plant, and plant height, were highly upregulated in drought tolerant genotypes. In contrast, two other genes, Rab-GDP dissociation inhibitor (Rab-GDI) and Transducin with WD40 repeats, associated with seed yield, showed repression in the same genotypes. These verified genes involved in the control of yield and yield-related traits can be used for marker-assisted selection to develop novel genotypes and new soybean cultivars tolerant to strong drought in Kazakhstan and in other countries with similar conditions.

Diversity array technology (DArT)↗

Joint oligogenic segregation and linkage analysis using bayesian Markov chain Monte Carlo methods.

One of the most challenging areas in human genetics is the dissection of quantitative traits. In this context, the efficient use of available data is important, including, when possible, use of large pedigrees and many markers for gene mapping. In addition, methods that jointly perform linkage analysis and estimation of the trait model are appealing because they combine the advantages of a model-based analysis with the advantages of methods that do not require prespecification of model parameters for linkage analysis. Here we review a Markov chain Monte Carlo approach for such joint linkage and segregation analysis, which allows analysis of oligogenic traits in the context of multipoint linkage analysis of large pedigrees. We provide an outline for practitioners of the salient features of the method, interpretation of the results, effect of violation of assumptions, and an example analysis of a two-locus trait to illustrate the method.

Bayes Theorem↗

Identity-by-descent and association mapping of a recessive gene for Hirschsprung disease on human chromosome 13q22.

Hirschsprung disease (HSCR) is a congenital disorder of unknown etiology characterized by the absence of enteric ganglia in the distal colon. We have ascertained a large, inbred, Mennonite kindred which demonstrates a high incidence of Hirschsprung disease (HSCR). Genealogical analysis of all kinship relationships identified a single common ancestral couple for all parents of affected offspring. Segregation analysis yielded a segregation ratio of 10.67% for males and 5.45% for females. We searched for locations of the gene(s) responsible for HSCR in this pedigree by genotyping three small multicase families and locating genomic regions demonstrating identity-by-descent followed by linkage disequilibrium analysis of 28 additional nuclear families. Based on this novel strategy, we report the mapping of a new locus for HSCR to chromosome 13q22. Nine microsatellite markers spanning 10 cM in this region were genotyped on thirty-one nuclear families. Significant nonrandom association was detected with alleles at markers D13S162, D13S160, D13S170, and AFM240zg9. In addition, our studies reveal preliminary evidence for a genetic modifier of HSCR in this kindred on chromosome 21q22.

Chromosome Mapping↗

Assignment of the locus order DXS28-DXS67-DMD as a spin-off from diagnostic DNA marker analysis in a family with Duchenne muscular dystrophy.

During diagnostic segregation analysis for seven DNA markers, linked to and flanking the locus for Duchenne muscular dystrophy (DMD), a family was identified in which a boy with a recombinant X chromosome had inherited his maternal grandmother's alleles at the loci DXS43 (D2/Pvu II) and DXS28 (C7/Eco RV), and his maternal grandfather's alleles at DXS67 (B24/Msp I) and DXS84 (754/Pst I). Combined with earlier data this finding strongly suggests the locus order DXS28-DXS67-DMD. Another recombination event, identified in the same family, supports the previously established order DMD-DXS84-OTC. The diagnostic importance of flanking markers, and the likelihood of false diagnostic conclusions due to possible double crossovers, with and without demonstrable neighbouring single crossover events, are discussed.

Genetic Linkage↗

AFLP markers linked to resistance against Striga gesnerioides race 1 in cowpea (Vigna unguiculata).

Amplified fragment length polymorphism (AFLP) analysis was used in combination with bulked segregant analysis (BSA) to identify molecular markers linked to two cowpea (Vigna unguiculata (L.) Walp.) genes conferring resistance to Striga gesnerioides race 1. After AFLP analysis of an F2 population derived from a cross between the resistant cultivar Gorom and the susceptible cultivar Tvx 3236, seven AFLP markers were identified that are linked to Rsg3, the gene conferring race I resistance in 'Gorom'. The distances between these markers and Rsg3 ranged from 9.9 to 2.5 cM, with two markers, E-AGA/M-CTA460 and E-AGA/M-CAG300, flanking Rsg3 at 2.5 and 2.6 cM, respectively. Analysis of a second F2 population derived from the cross between 'Tvx 3236' and the resistant cultivar IT81D-994 identified five AFLP markers linked to the race 1 resistance gene 994-Rsg present in 'IT81D-994'. The two markers showing the tightest linkage to the 994-Rsg locus were E-AAG/M-AAC450 and E-AAG/M-AAC150 at 2.1 and 2.0 cM, respectively. Two of the markers linked to 994-Rsg, E-AGA/M-CAG300 and E-AGA/M-CAG450, were also linked to Rsg3. The identification of molecular markers in common between the two sources of race 1 resistance suggests that either Striga resistance genes are clustered in these plants or that these loci are allelic. Mapping of the resistance loci within the cowpea genome revealed that three markers linked to Rsg3 and (or) 994-Rsg are located on linkage group 6.

Chromosome Mapping↗

Atherogenic lipoprotein phenotype. A proposed genetic marker for coronary heart disease risk.

In a community-based study of 301 subjects from 61 nuclear families, two distinct phenotypes (denoted A and B) were identified by nondenaturing gradient gel electrophoretic analysis of low density lipoprotein (LDL) subclasses. Phenotype A was characterized by predominance of large, buoyant LDL particles, and phenotype B consisted of a major peak of small, dense LDL particles. Previous analysis of the family data by complex segregation analysis demonstrated that these phenotypes appear to be inherited as a single-gene trait. In the present study, the phenotypes were found to be closely associated with variations in plasma levels of other lipid, lipoprotein, and apolipoprotein measurements. Specifically, phenotype B was associated with increases in plasma levels of triglyceride and apolipoprotein B, with mass of very low and intermediate density lipoproteins, and with decreases in high density lipoprotein (HDL) cholesterol, HDL2 mass, and plasma levels of apolipoprotein A-I. Thus, the proposed genetic locus responsible for LDL subclass phenotypes also results in an atherogenic lipoprotein phenotype.

Adolescent↗

A Novel SLC25A4 Variant Causing Mitochondrial Dysfunction, Myopathy and Cardiomyopathy: A Functional and Molecular Characterization.

SLC25A4, solute carrier family 25 member 4, gene is a member of the mitochondrial carrier subfamily within the solute carrier protein family. Pathogenic variants in SLC25A4 are associated with a spectrum of mitochondrial disorders that exhibit variable inheritance patterns and clinical manifestations. Specifically, dominantly inherited variants are typically associated with progressive external ophthalmoplegia with mitochondrial DNA deletions, recessively inherited variants are linked to myopathy and cardiomyopathy, and de novo variants can result in early-onset fatal disease presentations. In this study, we aimed to identify and characterize the disease-causing mutation(s) in a nine-year-old female patient from a consanguineous Saudi family. The patient was asymptomatic until the age of 3 years, when she presented with cardiomyopathy and myopathy. Comprehensive genetic analysis inclusive of whole exome sequencing and segregation analysis using Sanger sequencing identified an SLC25A4 variant (NM_001151.4: exon 2: c.112-1G>C) as the most likely cause of the disease. To assess transcript-level effects, we performed RT-PCR on RNA extracted from the patient's cultured lymphoblast cell lines (LCLs) and fibroblast cell lines (FCLs). RT-PCR analysis demonstrated that the variant causes aberrant splicing, resulting in a 6 bp in-frame deletion (p.Gln37_Val38del) in the ANT1 protein. Quantitative RT-PCR demonstrated reduced SLC25A4 transcript levels in both FCLs and LCLs. Quantitative PCR analysis of mitochondrial DNA demonstrated a trend toward increased mtDNA copy number in patient-derived FCLs compared with controls, suggesting a possible compensatory response to mitochondrial dysfunction. Furthermore, Seahorse assays revealed marked reductions in both oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in patient-derived FCLs compared with controls. These findings expand the molecular and functional spectrum of SLC25A4-associated disease and may inform clinical practice, including genetic interventions such as preimplantation genetic diagnosis, premarital genetic screening, targeted genetic counseling, and cascade testing of at-risk family members.

Humans↗

[Genetic analysis of the susceptibility to neurological manifestations in spinal osteochondrosis].

Complex genetic-mathematical analysis (component decomposition of the phenotype variance, segregation analysis, estimation of penetrance parameters) of 324 probands' families with neurologic manifestation of spinal osteochondrosis (3437 relatives of I-III degree) has been carried out is shown that the structure of liability to the disease studied is better approximated by semi-continuous phenotype model within the limits of which contribution of genetic factors reaches 80% (63-66% owing to autosomes and 14-17% owing to gonosomes) under considerable influence (20%) of environmental force (14% accidental and 6% systematic).

Age Factors↗

Familial antiphospholipid antibody syndrome: criteria for disease and evidence for autosomal dominant inheritance.

OBJECTIVE: To develop diagnostic criteria for a familial form of antiphospholipid antibody syndrome (APS), identify families with >1 affected member, examine possible modes of inheritance, and determine linkage to potential candidate genes. METHODS: Family members of probands with primary APS were analyzed for clinical and laboratory abnormalities associated with APS. Families with > or =2 affected members were analyzed by segregation analysis and typed for candidate genetic markers. RESULTS: Seven families were identified. Thirty of 101 family members met diagnostic criteria for APS. Segregation studies rejected both environmental and autosomal recessive models, and the data were best fit by either a dominant or codominant model. Linkage analysis showed independent segregation of APS and several candidate genes. CONCLUSION: Clinical and laboratory criteria are essential to identify the spectrum of disease associated with APS. We believe a set of criteria was developed that can precisely define affected family members with APS. Modeling studies utilizing these criteria strongly support a genetic basis for disease in families with APS and suggest that a susceptibility gene is inherited in an autosomal dominant pattern. However, in these families, APS was not linked with HLA, Fas, or other candidate genes, including beta2-glycoprotein 1, HLA, T cell receptor beta chain, Ig heavy chain, antithrombin III, Fas ligand, factor V, complement factor H, IgK, and Fas.

Adolescent↗

Genetic crosses reveal genomic loci responsible for virulence in Cryptosporidium parvum infection.

The relationship between parasite genotype and pathogenesis is largely unknown for Cryptosporidium, a leading cause of diarrheal disease in children. An array of parasites with similar genomes produces varied disease outcomes in different hosts. Here, we isolate and characterize Cryptosporidium parvum strains that show marked differences in virulence and persistence in mice. Taking advantage of the sexual life cycle of this eukaryotic pathogen, we use genetic crosses to discover the underlying chromosomal loci. Whole-genome sequencing and bulk segregant analysis of infection-selected progeny mapped three loci on chromosomes 2, 6, and 7 associated with the ability to colonize and persist in mice and the positions of drug resistance genes. The chromosome 6 locus encodes the hyper-polymorphic surface glycoprotein GP60. Reverse genetic studies in both parental strains demonstrate that GP60 controls parasite burden and virulence, but not persistence, and reveal the dominance of the less virulent allele, suggesting it restricts virulence.

Cryptosporidium parvum↗