X-linked recessive combined pituitary hormone deficiency is mapped to Xp22.3-Xp11 in a Chinese family

Genetic mutations have been identified in a modest proportion of patients with combined pituitary hormone deficiency (CPHD). We reported a 3-generation family consisting of 18 members, including 5 affected males (the proband, his 2 brothers, his cousin, and his maternal uncle; III1–III4, II8) suffered with CPHD. MRI of the pituitary gland showed hypoplasia of the pituitary gland in affected members. By 19 STR markers and linkage analysis, we found that the disease gene localized between the DXS987 and DXS1226 markers (LOD score = 2.408, θ = 0). All affected male patients inherited the same haplotype from the female carrier (I4). The proband's mother (II4) and her sister (II3, II6) were obligate female carriers. However, the unaffected males (II₇, II₉) in the family did not have this haplotype. These observations confirm a new X-linked recessive inherited disease in a Chinese family with CPHD and the pathogenic gene is mapped to Xp22.1–Xp11.     

HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination

MOTIVATION: Haplotype reconstruction is an essential step in genetic linkage and association studies. Although many methods have been developed to estimate haplotype frequencies and reconstruct haplotypes for a sample of unrelated individuals, haplotype reconstruction in large pedigrees with a large number of genetic markers remains a challenging problem. METHODS: We have developed an efficient computer program, HAPLORE (HAPLOtype REconstruction), to identify all haplotype sets that are compatible with the observed genotypes in a pedigree for tightly linked genetic markers. HAPLORE consists of three steps that can serve different needs in applications. In the first step, a set of logic rules is used to reduce the number of compatible haplotypes of each individual in the pedigree as much as possible. After this step, the haplotypes of all individuals in the pedigree can be completely or partially determined. These logic rules are applicable to completely linked markers and they can be used to impute missing data and check genotyping errors. In the second step, a haplotype-elimination algorithm similar to the genotype-elimination algorithms used in linkage analysis is applied to delete incompatible haplotypes derived from the first step. All superfluous haplotypes of the pedigree members will be excluded after this step. In the third step, the expectation-maximization (EM) algorithm combined with the partition and ligation technique is used to estimate haplotype frequencies based on the inferred haplotype configurations through the first two steps. Only compatible haplotype configurations with haplotypes having frequencies greater than a threshold are retained. RESULTS: We test the effectiveness and the efficiency of HAPLORE using both simulated and real datasets. Our results show that, the rule-based algorithm is very efficient for completely genotyped pedigree. In this case, almost all of the families have one unique haplotype configuration. In the presence of missing data, the number of compatible haplotypes can be substantially reduced by HAPLORE, and the program will provide all possible haplotype configurations of a pedigree under different circumstances, if such multiple configurations exist. These inferred haplotype configurations, as well as the haplotype frequencies estimated by the EM algorithm, can be used in genetic linkage and association studies. AVAILABILITY: The program can be downloaded from http://bioinformatics.med.yale.edu.     

The effect of triisopropyl phosphate on the mobility of surface concanavalin a receptors and on the locomotion of polymorphonuclear leucocytes

The non-phosphorylating organophosphorus compound triisopropyl phosphate, which is known to inhibit rabbit leucocyte locomotion, can stimulate the locomotion of guinea pig leucocytes under certain conditions. Different methods of preparing guinea pig leucocyte monolayers can give preparations with different proportions of motile cells. With preparations that contain relatively slowly moving cells triisopropyl phosphate increases the number of stationary cells without significantly affecting the speed of the cells that remain motile. Most rabbit leucocytes labelled with fluorescein-labelled concanavalin A form caps within 5–10 min at 37 °C. In contrast the rate of cap formation in guinea pig leucocytes is much slower and after 20 min many cells have only random patches. Triisopropyl phosphate accelerates cap formation in guinea pig leucocytes but not in rabbit leucocytes. The local anaesthetic nupercaine inhibits cap and patch formation in rabbit and guinea pig leucocytes. Inhibition of rabbit leucocyte locomotion is induced by concanavalin A at 1 μg/ml. These results are briefly related to the known effects of triisopropyl phosphate on the isolated leucocyte plasma membrane.     

Association of smoking behavior with an odorant receptor allele telomeric to the human major histocompatibility complex

Smoking behavior has been associated in two independent European cohorts with the most common Caucasian human leukocyte antigen (HLA) haplotype (A1-B8-DR3). We aimed to test whether polymorphic members of the two odorant receptor (OR) clusters within the extended HLA complex might be responsible for the observed association, by genotyping a cohort of Hungarian women in which the mentioned association had been found. One hundred and eighty HLA haplotypes from Centre d'Etude du Polymorphisme Humain families were analyzed in silico to identify single-nucleotide polymorphisms (SNPs) within OR genes that are in linkage disequilibrium with the A1-B8-DR3 haplotype, as well as with two other haplotypes indirectly linked to smoking behavior. A nonsynonymous SNP within the OR12D3 gene (rs3749971(T)) was found to be linked to the A1-B8-DR3 haplotype. This polymorphism leads to a (97)Thr --> Ile exchange that affects a putative ligand binding region of the OR12D3 protein. Smoking was found to be associated in the Hungarian cohort with the rs3749971(T) allele (p = 1.05 x 10(-2)), with higher significance than with A1-B8-DR3 (p = 2.38 x 10(-2)). Our results link smoking to a distinct OR allele, and demonstrate that the rs3749971(T) polymorphism is associated with the HLA haplotype-dependent differential recognition of cigarette smoke components, at least among Caucasian women.     

The swine leucocyte antigen (SLA) complex and Sinclair swine cutaneous malignant melanoma

Cutaneous malignant melanoma of Sinclair swine (SSCM) is an inherited neoplasm present at birth in a majority of affected animals. We have characterized the swine leucocyte antigen (SLA) complex of the Sinclair herd at Texas A & M University using a one-way mixed lymphocyte test and found that one particular haplotype, arbitrarily identified as haplotype B, is associated with the expression of SSCM. Only a single dose of the B haplotype is required for a dominant allele at a 'tumour initiator' locus to be fully penetrant. In addition, swine homozygous for haplotype B develop more primary tumours between birth and weaning than those heterozygous for the B haplotype. Taken together, these findings indicate that tumour initiation, in utero, and expression between birth and weaning may involve different mechanisms.     

The swine leucocyte antigen (SLA) complex and Sinclair swine cutaneous malignant melanoma

Summary. Cutaneous malignant melanoma of Sinclair swine (SSCM) is an inherited neoplasm present at birth in a majority of affected animals. We have characterized the swine leucocyte antigen (SLA) complex of the Sinclair herd at Texas A & M University using a one-way mixed lymphocyte test and found that one particular haplotype, arbitrarily identified as haplotype B , is associated with the expression of SSCM. Only a single dose of the B haplotype is required for a dominant allele at a 'tumour initiator' locus to be fully penetrant. In addition, swine homozygous for haplotype B develop more primary tumours between birth and weaning than those heterozygous for the B haplotype. Taken together, these findings indicate that tumour initiation, in utero , and expression between birth and weaning may involve different mechanisms.     

Inherited deficiency of the sixth component of complement: a silent or null gene

Four families have been studied, some members of which have inherited deficiency of the sixth component of complement. The genetically determined electrophoretic variants of C6 were evaluated in all family members. Seven individuals were found who did not have the variant found in the serum of the parent from whom they inherited the deficiency. It is inferred that the isolated low levels of C6 in these individuals results from the heterozygous state of a normal C6 variant gene and a silent or null C6 gene; the genes determining electrophoretic variants and the low serum levels of C6 are allelic.     

Failure of OKT3 monoclonal antibody to induce lymphocyte mitogenesis: a familial defect in monocyte helper function

Monoclonal antibodies to the T3 molecule on human T cells have mitogenic activity. Although anti-T3 antibodies of the IgG1 subclass (e.g., UCHT1) induce mitogenesis in lymphocyte cultures from only 60 to 70% of normal donors, antibodies of Ig2a subclass (e.g., OKT3) invariably have been found to be mitogenic in all subjects tested up to the present. This paper describes a family (a mother, six daughters, and one son) in which five members failed to respond mitogenically to OKT3 although the proportion of OKT3-reactive cells in their peripheral blood was normal. Mitogenic responses to PHA, Con A, and PWM were normal. Five members comprising four OKT3 nonresponders were also unresponsive to UCHT1. Unresponsiveness to OKT3 and unresponsiveness to UCHT1 were not absolutely linked to each other, nor were they linked to an HLA haplotype inherited from the mother. Upon stimulation by OKT3, lymphocyte preparations from OKT3-nonresponders failed to produce interleukin 2 (IL 2) and to display IL 2 receptors. OKT3 unresponsiveness was due to defective monocyte help: thus, responsiveness to OKT3 of T cells from an OKT3-nonresponder was restored by the addition of monocytes from an HLA-identical sister who had a normal response to OKT3. Inversely, T cells from the OKT3 responder had no reactivity to OKT3 when cultured in the presence of monocytes from an HLA-identical, OKT3-nonresponsive sister. Unresponsiveness to OKT3 could not be overcome by the addition of phorbol myristate acetate to the cultures. These data on a familial, non-HLA-linked deficiency of monocytes to exert their auxiliary function provide better insight into the mechanism of anti-T3-induced T cell activation.     

一个中国汉族皮肤和粘膜多发静脉血管畸形家系的单倍型分析

根据患者的临床体征以及家系的遗传方式,文章对一个中国汉族皮肤和粘膜多发静脉血管畸形(Mucocutaneous venous malformations,VMCM)家系进行了临床诊断。家系中连续5代都有患者,男女患者比例约1:1,为常染色体显性遗传方式。患者皮肤、口腔粘膜、舌头以及四肢等处可见蓝紫色、突出皮面、质硬、压之不褪色的瘤体,组织病理学显示,静脉血管的管腔极不规则,部分管壁存在缺失,部分管壁明显增厚。患者无消化道出血史,无心脏和脑部异常,临床诊断为VMCM。为了进行致病基因的定位和单倍型分析,采集了家族中26人的外周血并提取基因组DNA,并设计微卫星引物进行了连锁和单倍型分析。两点间连锁分析的结果表明,在D9S1121处有最大LOD值为Z=5.38(θ=0.00),单倍型分析的结果提示,致病基因定位于9号染色体短臂上D9S1121和D9S161之间约7 cM的范围内。文章首次报道了中国汉族VMCM家系,其致病基因定位定位于9p,与已报道的欧洲家系相同。用4个微卫星标记D9S1121、D9S 169、D9S161和D9S248确定了该家系致病基因的单倍型,为不同种族和人群VMCM疾病相关研究提供参考。     

Haplotype analysis for mucocutaneous venous malformations in a Chinese Han ethnic family

A Chinese Han ethnic family with mucocutaneous venous malformations (VMCM) was investigated. This family has autosomal dominantly inherited VMCM in five generations, and the offspring has a 50% risk of this inherited disorder. Affected individuals have small, spongy, and multiple vascular lesions, which often locate in the skin, oral mucosa, and upper and lower extremities. None of the family members had gastrointestinal bleeding, central nervous system involvement and cardiac defects. Pathological analysis showed that the veins have irregular vascular space and walls with variable thickness. All phenotypes of the patients displayed the basic characters of VMCM. To analyze the genetic locus and haplotype, genomic DNA of 26 family members was obtained from peripheral leukocytes, and the linkage analysis and haplotypes analysis were performed using microsatellites markers. The results of two-point linkage analysis and haplotype analysis showed that the disease-causing gene located within a 7 cM region between D9S1121 and D9S161 on the short arm of chromosome 9. The study firstly reported the Chinese family with VMCM, which disease-causing gene is located in 9p, consistent with western VMCM families reported. Four flanking markers, D9S1121, D9S169, D9S16 and D9S248, were used to define the linkage haplotypes in the family, which can provide useful informaion for researchers to study VMCM in different racial background.     

Two unlinked loci controlling the sex of blue tilapia (Oreochromis aureus)

Sex determination in the blue tilapia (Oreochromis aureus) is thought to be a WZ-ZZ (female heterogametic) system controlled by a major gene. We searched for DNA markers linked to this major gene using the technique of bulked segregant analysis. We identified 11 microsatellite markers on linkage group 3 which were linked to phenotypic sex. The putative W chromosome haplotype correctly predicts the sex of 97% of male and 85% of female individuals. Our results suggest the W locus lies within a few centimorgans of markers GM354, UNH168, GM271 and UNH131. Markers on LG1 also showed a strong association with sex, and indicate the segregation of a male-determining allele in this region. Analysis of epistatic interactions among the loci suggests the action of a dominant male repressor (the W haplotype on LG 3) and a dominant male determiner (the Y haplotype on LG1). These markers have immediate utility for studying the strength of different sex chromosome alleles, and for identifying broodstock carrying copies of the W haplotype.     

Neither season nor sex affects the cost of terrestrial locomotion in a circumpolar diving duck: the common eider (Somateria mollissima)

Locomotion accounts for a significant proportion of the energy budget in birds, and selection is likely to act on its economy, particularly where energy conservation is essential for survival. Birds are capable of different forms of locomotion, such as walking/running, swimming, diving and flying, and adaptations for these affect the energetic cost [cost of locomotion (CoL)] and kinematics of terrestrial locomotion. Furthermore, seasonal changes in climate and photoperiod elicit physiological and behavioural adaptations for survival and reproduction, which also influence energy budget. However, little is understood about how this might affect the CoL. Birds are also known to exhibit sex differences in size, behaviour and physiology; however, sex differences in terrestrial locomotion have only been studied in two cursorially adapted galliform species in which males achieved higher maximum speeds, and in one case had a lower mass-specific CoL than females. Here, using respirometry and high-speed video recordings, we sought to determine whether season and sex would affect the CoL and kinematics of a principally aquatic diving bird: the circumpolar common eider (Somateria mollissima). We demonstrate that eiders are only capable of a walking gait and exhibit no seasonal or sex differences in mass-specific CoL or maximum speed. Despite sharing identical limb morphometrics, the birds exhibited subtle sex differences in kinematic parameters linked to the greater body mass of the males. We suggest that their principally aquatic lifestyle accounts for the observed patterns in their locomotor performance. Furthermore, sex differences in the CoL may only be found in birds in which terrestrial locomotion directly influences male reproductive success.     

High resolution mapping of OCA2 intragenic rearrangements and identification of a founder effect associated with a deletion in Polish albino patients

Oculocutaneous albinism type 2 (OCA2) represents about 30% of OCA worldwide. Using quantitative multiplex fluorescent PCR and very high-resolution array-CGH focussed on the OCA2 gene and surrounding regions in 15q12, we identified new rearrangements. Deletion 1, encompassing exons 3-20, was present in three patients (including one in the homozygous state), and Deletion 2 (exons 1-20) was found in one patient (heterozygous state). The duplication (exons 3-20) was found in one patient in the homozygous state. Using 14 microsatellite markers we determined haplotypes associated with these rearrangements. Deletion 1 was associated with the same haplotype in three patients who were all of Polish origin, which is strongly in favour of a founder effect. Deletion 2 was associated with a distinct haplotype. The homozygous duplication was inherited from the two unrelated parents of the patients on two different haplotypes. Analysis of the sequences around the breakpoints of these rearrangements showed that all occurred within complex arrays of repetitive sequences. The combined use of very high-resolution array-CGH and of microsatellites (including new intragenic ones described here) constitutes a powerful approach for the precise characterization of OCA2 rearrangements, which have been found in more than 20% of OCA2 patients.     

Identification of a sex-determining region in Nile tilapia (Oreochromis niloticus) using bulked segregant analysis

Sex determination in the Nile tilapia (Oreochromis niloticus) is thought to be an XX-XY (male heterogametic) system controlled by a major gene. We searched for DNA markers linked to this major locus using bulked segregant analysis. Ten microsatellite markers belonging to linkage group 8 were found to be linked to phenotypic sex. The putative Y-chromosome alleles correctly predict the sex of 95% of male and female individuals in two families. Our results suggest a major sex-determining locus within a few centimorgans of markers UNH995 and UNH104. A third family from the same population showed no evidence for linkage of this region with phenotypic sex, indicating that additional genetic and/or environmental factors regulate sex determination in some families. These markers have immediate utility for studying the strength of different Y chromosome alleles, and for identifying broodstock carrying one or more copies of the Y haplotype.     

X连锁隐性遗传聋哑（deaf-mute）家系的遗传学特征分析

在进行中国人群的遗传性耳聋发病情况的调查中,发现了一个5代隔代遗传的聋哑家系（L021家系）。研究中调查家系成员64人,对其中的31人进行了系统的听力学检查,发现聋哑男性8位,听力表型为全聋及极重度聋,获得家系成员的血样31人份。家系图谱分析显示该家系为X连锁隐性遗传性耳聋家系,为先天性聋哑疾病分子病理机制的研究提供了模板。     

Geographic distribution and origin of the chloroplast T/C‐type in Quercus mongolica var. crispula in northeastern Japan

In order to investigate the historical expansion of common oaks (Quercus sect. Prinus) in the northeastern part of Japan, the relation between the chloroplast haplotypes (I and II) in Quercus mongolica var. crispula and the chloroplast types (T‐ and C‐type) were examined. Complete linkage between haplotype II and chloroplast C‐type was found. The chloroplasts examined in the oak species collected from Sakhalin and Primorski Krai, Russia, and Harbin, China were all T‐type. This suggests that the T to C mutation had occurred in haplotype II in Japan. Neither of haplotype I nor haplotype II was found outside Japan, suggesting both occurred in Japan independently from an ancestral haplotype VI. Haplotype I, which has been known only in Mount Hayachine within Honshu, is distributed southward to the Kanto district, where refugia might have occurred during glaciations.     

The detection of nonhybrid, trisomic, and triploid offspring in sexual progeny of a mating of Phytophthora infestans.

Eighty single-oospore offspring of Phytophthora infestans from a mating of isolates, which had previously been analyzed for segregation of avirulence/virulence, were assessed for the inheritance of 20 RFLP markers. Three offspring were triploid; they inherited three alleles at all loci where this could be detected and when heterozygous, showed unequal intensities of hybridization with most probes. Twenty-four offspring were trisomic, as each had three doses of one or a few markers, evident from their inheritance of three alleles or from unequal hybridization to one probe. Coinheritance of the extra allele(s) and mitochondrial haplotype in the majority of trisomic offspring suggested that meiosis in oogonia was more aberrant than in antheridia. Linkage analysis was performed on 50 offspring, which were assumed to be euploid; six small linkage groups were detected and several avirulence loci were found to be linked. The origins of aberrant offspring are discussed.     

Analysis of HLA and Disease Susceptibility: Chromosome 6 Genes and Sex Influence Long-QT Phenotype

The long-QT (LQT) syndrome is a genetically complex disorder that is characterized by syncope and fatal ventricular arrhythmias. LQT syndrome, as defined by a prolonged electrocardiographic QT interval, has a higher incidence in females than in males and does not exhibit Mendelian transmission patterns in all families. Among those families that are nearly consistent with Mendelian transmission, linkage between a locus for LQT syndrome and the H-ras-1 locus on the short arm of chromosome 11 has been reported in some families but not in others. Earlier analyses suggesting that LQT syndrome might be caused by a gene in the HLA region of chromosome 6 were not confirmed by standard linkage analyses. Here, we present an analysis of HLA haplotype sharing among affected pedigree members, showing an excess of haplotype sharing in a previously published Japanese pedigree and possibly also in 15 families of European descent. The haplotypes shared by affected individuals derive from both affected and unaffected parents. In an analysis of independent (unrelated) HLA haplotypes, we also found a nonrandom distribution of HLA-DR genes in LQT syndrome patients compared with controls, suggesting an association between the LQT phenotype and specific HLA-DR genes. Our data indicate that DR2 has a protective effect and, particularly in males, that DR7 may increase susceptibility to the LQT syndrome. Thus, LQT syndrome may be influenced by genes on chromosomes 11 and 6, possibly with a sex-specific effect. These results provide a model for an effect of HLA-region genes inherited from either parent on the expression of an illness that may be determined principally by alleles at loci not linked to HLA.     

Genetic analysis of the H-2D region using a new intra-D-region recombinant mouse strain

A rare D-region recombination event which gave rise to the B10.RQDB major histocompatibility complex haplotype has been examined to ascertain the nature of the crossover and to determine which class I genes are present in the new alignment of D-region genes. Serologic analysis have shown that the B10 . RQDB major histocompatibility complex recombinant mouse inherited the H-2Dd gene from the B10.T(6R) parental line and the H-2Db gene from the B10.A(2R) parental line, representing the first example of an intra-D-region crossover resulting from an intercross. Previous molecular genetic analyses of the d and b haplotypes revealed structural diversity in the organization of their D-region gene clusters. Hence, the D region is comprised of five class I genes in the d haplotype and only one in the b haplotype. Because allelic relationships among the various D-region genes are not defined, either a homologous or nonhomologous alignment of genes has generated the RQDB crossover. Therefore, the possibility that all three D-region antigen-presenting molecules (Dd, Ld, and Db) might be encoded by the RQDB haplotype was examined. Fluorescence-activated cell sorter and cytotoxic T lymphocyte analyses revealed no detectable levels of H-2Ld cell-surface expression, confirming earlier studies with antibody-mediated cytotoxicity and immunoprecipitation. Southern blot analysis localized the recombination point to within a 1-kb region at the centromeric end of the H-2Ld gene on the B10 . T(6R) chromosome in a region of high homology to the H-2Db gene on the B10 . A(2R) chromosome. Together, these studies define the D region of the RQDB haplotype as containing the five class I genes: Dd, D2d, D3d, D4d, and Db. In addition to providing insight into rare recombination events in the D region, the B10.RQDB mouse should be a useful tool for exploring the function of D-region genes.