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PubMed1994

Prenatal testosterone levels in XXY and XYY males.

It has been postulated that behavioural differences between normal males and those with an additional X or Y chromosome may be related to pre- or postnatal hormonal variations. The prenatal hormone status was investigated using amniotic fluid obtained at antenatal diagnosis between 16 and 20 weeks gestation from fetuses with sex chromosome abnormalities and from controls of the same gestational age. After log transformation, the (geometric) mean testosterone levels were XY 439.4 pmol/l, range 165-1,027 (n = 29), XYY 490.7 pmol/l, range 224-1,092 (n = 20); and XXY 419 pmol/l, range 87-1,021 (n = 20). There were no significant differences between the three male groups and all three were significantly higher than the XX fetuses at 147.0 pmol/l, range 41-474 (p < 0.001). These findings give no support to the hypothesis that prenatal testosterone levels contribute to later behavioural characteristics.

Amniotic Fluid↗

PubMed2001

All three splice variants of the human sarco/endoplasmic reticulum Ca2+-ATPase 3 gene are translated to proteins: a study of their co-expression in platelets and lymphoid cells.

The molecular cloning of two previously unknown human sarco/endoplasmic reticulum Ca(2+)-ATPase 3 (SERCA3) 3'-end transcripts, 3b and 3c, has been recently published. Data were lacking, however, for the presence of these SERCA3 variants in different tissue or cell types at the protein level. Here we report the co-expression of three human SERCA3 protein isoforms in platelets and T lymphoid Jurkat cells. Isoform-specific polyclonal anti-peptide antibodies have been generated that recognize specifically the SERCA3a, 3b or 3c splice variants at their C-termini, and this has been confirmed by peptide-competition experiments as well. None of these antibodies cross-reacted with the housekeeping SERCA2b isoform co-expressed endogenously with SERCA3 proteins in non-muscle cells. Although all three SERCA3 isoforms could be detected in platelets, the 3a form was the most abundantly expressed species. Its size matched the apparent size of SERCA3a over-expressed in HEK-293 cells. Immunoprecipitation of the SERCA3 variants from platelet membranes using a PL/IM 430-affinity matrix provided evidence that the putative pan-anti-SERCA3 antibody, PL/IM 430, recognizes all SERCA3 protein isoforms. The epitope for the PL/IM 430 antibody could be localized in a 40 kDa N-terminal tryptic fragment common to all three SERCA3 variants. Comparative Western-blot analysis showed that the expression level of the SERCA3a, 3b and 3c isoforms was more than 10 times lower in Jurkat cells than in platelets, whereas expression of the ubiquitous SERCA2b was nearly identical. This work highlights new Ca(2+)-transporting proteins of haematopoietic cells and provides specific antibodies for their detection.

Alternative Splicing↗

PubMed2004

Gene expression, synteny, and local similarity in human noncoding mutation rates.

The human genome is organized with regard to many features such as isochores, Giemsa bands, clusters of genes with similar expression patterns, and contiguous regions with shared evolutionary histories (synteny blocks). In addition to these genomic features, it is clear that mutation rates also vary across the human genome. To address how mutation rates and genomic features are related, we analyzed substitution rates at three classes of putatively neutral noncoding sites (nongenic, intronic, and ancestral repeats) in approximately 14 Mb of human-chimpanzee alignments covering human chromosome 7. Patterns of mutation rate variation inferred from substitution rate variation differ among the three site classes. In particular, we find that intronic mutation rates are strongly affected by the breadth of expression of the genes in which they reside, with broadly expressed genes exhibiting low mutation rates, probably as a consequence of the transcription-coupled repair process acting in the germ line. All site classes show significant local similarities in mutation rate at the megabase scale, and regional similarities in nongenic mutation rate covary with blocks of synteny between the human and mouse genomes, indicating that the evolutionary history of a genomic region is an important determinant of mutation rate.

Animals↗

PubMed1986

Non-A, non-B hepatitis related AN6520 Ag is a normal cellular protein mainly expressed in liver. II.

Detection of AN6520 Ag/Ab in human sera had indicated a close association with non-A, non-B hepatitis (NANBH). In this study, we investigated the immunochemical nature of AN6520 Ag and measured the amounts in various human and chimpanzee organs in order to clarify the association with NANBH. AN6520 Ag was found to be composed of polypeptide(s) with an apparent molecular weight of 45,000 daltons (45 kD), which are noncovalently linked together. Human antibodies in convalescent sera from NANBH patients as well as monoclonal antibodies were found to recognize only the high-order structure of the antigen, whereas rabbit antibody recognized both the high-order structure and the reduced form of 45 kD polypeptide(s). AN6520 Ag could be detected in most of the livers tested including those without any liver damage and fetal livers; their amounts varied considerably from each other. The antigen could be detected also in organs other than liver, but in contrast to liver, the amounts were small and did not vary as much between individuals. From the data of immunoblotting using rabbit antibody, our observed variation of antigen content in liver was considered to be due to the difference in expression of 45 kD polypeptide(s). Although no specific relationship was found between the amount of the antigen in liver and NANBH, the antigen was found to increase several times in livers of chimpanzees after the inoculation of NANBH virus. These data suggest that AN6520 Ag is a normal cellular protein existing mainly in liver and that its quantity may vary under some conditions such as NANBH.

Adult↗

PubMed2006

Sequence diversity at the proximal 14q32.1 SERPIN subcluster: evidence for natural selection favoring the pseudogenization of SERPINA2.

The superfamily of serine protease inhibitors (SERPINs) plays a key role in controlling the activity of proteinases in diverse biological processes. alpha1-antitrypsin (SERPINA1), the most studied member of this family, is encoded by a gene located within the proximal 14q32.1 SERPIN subcluster, together with the highly homologous alpha1-antitrypsin-like sequence (SERPINA2), which was previously proposed to be a pseudogene. Here, we performed a resequencing study encompassing both SERPINA1 and SERPINA2 as well as the adjacent gene coding for corticosteroid-binding globulin (SERPINA6) in samples from Europe and West Africa. In the African sample, we found that a common haplotype carrying a 2-kb deletion in the SERPINA2 gene is associated with remarkable long-range homozygozity as if it was quickly driven to high frequency by natural selection acting on an advantageous variant. An analysis of the HapMap Phase I data for the Yoruba sample confirmed that variation in this subcluster carries a strong signal of positive selection. We also show that the SERPINA2 gene is expressed and probably encodes a functional SERPIN. Finally, comparisons with orthologous sequences in nonhuman primates showed that SERPINA2 is present in some great apes, but in chimpanzees it was lost by a deletion event independent from that observed in humans. In agreement with the "less is more" hypothesis, we propose that loss of SERPINA2 is an ongoing process associated with a selective advantage during recent primate evolution, possibly because of a role in fertility or in host-pathogen interactions.

Africa↗

PubMed2003

[Spatial heterogeneity of vegetation and soil characteristics in oasis-desert ecotone].

The spatial distribution of bio- and abiotic factors in ecosystem has the features of spatial heterogeneity in general, and spatial heterogeneity is important in the function and process of ecosystem at a variety of scales. In this paper, semivariance theory and methods were used to study the degree, composition, scale and pattern of spatial heterogeneity of vegetation coverage and soil environment factors, and their relationships in the Fukang oasis-desert ecotone of Xinjiang. With block kriging in the studied area of sampling, the spatial pattern of each factor was expressed in three dimensions as well. The results indicated that except the little spatial autocorrelation of salt salinity, there existed a spatial autocorrelation above mean of the other factors, and the spatial variation was mainly limited to smaller scales. The vegetation coverage, for which auto-correlated spatial heterogeneity was a main component, had a high degree of spatial heterogeneity with obvious spatial pattern at the scale of 3 km. From the perspective of spatial distributions, there existed a remarkable difference between soil holard and soil pH value in the studied area. Besides this, the higher value areas interleaved with the lower ones, significant positive correlations were observed between herbage coverage and soil factors (surface SH and SPH), and shrub coverage depended on the deep SH. The difference of spatial heterogeneity and pattern between SC and HC indicated the different ecological function and process in the ecosystem.

Desert Climate↗

PubMed2004

Brain structure variation in great apes, with attention to the mountain gorilla (Gorilla beringei beringei).

This report presents data regarding the brain structure of mountain gorillas (Gorilla beringei beringei) in comparison with other great apes. Magnetic resonance (MR) images of three mountain gorilla brains were obtained with a 3T scanner, and the volume of major neuroanatomical structures (neocortical gray matter, hippocampus, thalamus, striatum, and cerebellum) was measured. These data were included with our existing database that includes 23 chimpanzees, three western lowland gorillas, and six orangutans. We defined a multidimensional space by calculating the principal components (PCs) from the correlation matrix of brain structure fractions in the well-represented sample of chimpanzees. We then plotted data from all of the taxa in this space to examine phyletic variation in neural organization. Most of the variance in mountain gorillas, as well as other great apes, was contained within the chimpanzee range along the first two PCs, which accounted for 61.73% of the total variance. Thus, the majority of interspecific variation in brain structure observed among these ape taxa was no greater than the within-species variation seen in chimpanzees. The loadings on PCs indicated that the brain structure of great apes differs among taxa mostly in the relative sizes of the striatum, cerebellum, and hippocampus. These findings suggest possible functional differences among taxa in terms of neural adaptations for ecological and locomotor capacities. Importantly, these results fill a critical gap in current knowledge regarding great ape neuroanatomical diversity.

Animals↗

PubMed2005

Molecular markers distinguish bone marrow mesenchymal stem cells from fibroblasts.

To characterize mesenchymal stem cells (MSC), we compared gene expression profiles in human bone marrow MSC (11 lines) and human fibroblasts (4 lines) by RT-PCR and real time PCR. Messenger RNA levels of MHC-DR-alpha, MHC-DR-beta, MHC-DR-associated protein CD74, tissue factor pathway inhibitor-2, and neuroserpin were much higher in MSC than in fibroblasts, even in the presence of large interindividual variations. Those of adrenomedullin, apolipoprotein D, C-type lectin superfamily member-2, collagen type XV alpha1, CUG triplet repeat RNA-binding protein, matrix metalloproteinase-1, protein tyrosine kinase-7, and Sam68-like phosphotyrosine protein/T-STAR were lower in MSC than in fibroblasts. FACS analysis showed that cell surface expression of MHC-DR was also higher in MSC than in fibroblasts. MHC-DR expression decreased after osteogenic differentiation, whereas the expression of adrenomedullin-a potent stimulator of osteoblast activity-along with collagen XV alpha1 and apolipoprotein D increased after osteogenic differentiation. The marker genes identified in this study should be useful for characterization of MSC both in basic and clinical studies.

Biomarkers↗

PubMed2004

Transcriptional repression mechanisms of nucleolus organizer regions (NORs) in humans and chimpanzees.

Polymorphisms related to transcriptional inactivation of nucleolus organizer regions (NORs) have long been described in many animals, particularly humans. However, the precise aetiology of such variations is not always clear. We conducted analyses to investigate the repression mechanisms in humans and chimpanzees using FISH (fluorescence in situ hybridisation) with 18S rDNA, Ag-NOR (silver nitrate) staining, C-banding, and the in situ nick translation technique with the HpaII restriction enzyme. Examination of 48 humans and 46 chimpanzees suggested that there are at least three different mechanisms that produce inactivation of NORs. These include: (1) elimination of rDNA; (2) DNA methylation: (3) gene silencing due to position effects induced by heterochromatin (C-bands) and/or telomeres.

Animals↗

PubMed2002

Brief communication: arboreal bipedalism in Bwindi chimpanzees.

Evidence of the form and function of bipedal behavior in nonhuman primates provides critical evidence to test theories about the origins of hominid bipedalism. Bipedalism has long been considered an evolutionarily interesting but rare behavior in wild chimpanzees. During May 2001, chimpanzees of the Ruhija community in the Bwindi Impenetrable National Park, Uganda, engaged in an exceptional frequency of arboreal bipedalism when feeding in large Ficus trees. Seventy-eight bipedal bouts of at least 5 sec duration were recorded for the entire community (0.49 bouts/hr), with a mean duration of 13.7 sec (+/-1.6 sec). The animals employed many variations on the bipedal postural theme, ranging from erect standing on the largest substrates while grasping overhead limbs for support, to standing on one leg while suspending the other leg in space, to extended-lean standing, in which bipedal standing transitioned into horizontal arm-leg suspension as the animal reached for more distant fruits. Bipedalism was used as part of a behavioral repertoire that integrated brachiation, four-limbed suspension, and forelimb-supported standing for effective small-fruit foraging. These observations suggest that under certain ecological conditions, arboreal bipedalism can be an important posture for wild chimpanzees, and may have been an important behavioral precursor to full terrestrial bipedalism.

Adaptation, Physiological↗

PubMed1993

Diagnosis of gastrointestinal T-cell lymphomas in routinely processed tissues.

Diagnosis of primary gastrointestinal T-cell lymphomas is often problematic because lymphoma may not be suspected clinically or on resection, and tissue may not be frozen for immunophenotyping. Furthermore, ulceration and inflammation and the polymorphous character of the lesions makes evaluation difficult. Only approximately 150 cases have been reported, fewer than 20 from North America. We have tried to establish a reliable approach to the diagnosis of gastrointestinal lymphomas of T-cell phenotype in routinely processed tissue. Sections from five primary gastrointestinal T-cell lymphomas were stained with a panel of 13 antibodies reactive in routinely fixed, paraffin-embedded tissue. These included antibodies to pan-T- and pan-B-cell antigens (CD3, CD20), B- and T-cell-associated antigens (CD43, CD45R0; CDw75, CD74), antigens expressed by activated T-cells (HLA-DR, CD30), leukocyte antigens (CD45, CD15), and macrophage markers (MAC-387, HAM-56). All stained positively with T-cell markers MT-1 and Leu-22, four with UCHL-1, and three with anti-CD3 polyclonal antibody. B-cell markers identified by L-26 and LN-1 were negative in all five, whereas LN-2 was expressed in two. Two expressed HLA-DR; all were Ber-H2 negative. Two had an abnormal phenotype: one was Leu-M1 positive, and one LCA negative. Ten B-cell gastrointestinal lymphoma controls were negative for MT-1, Leu-22, and CD3, and nine were negative for UCHL-1. Nine were positive for the B-cell marker L-26, eight for LN-2, and seven for LN-1. All tumors were negative for monocyte-macrophage markers. This antibody panel provides a reliable means for identifying gastrointestinal T-cell lymphomas in paraffin sections. Use of a panel is advisable because of variation in expression and preservation of antigens, and to detect abnormal phenotypes. Application of this approach may facilitate the diagnosis of gastrointestinal T-cell lymphomas both prospectively and in archival material, and thereby encourage studies of the behavior and treatment of these neoplasms.

Aged↗

PubMed1997

[External assessment of analytic quality in hematology: a necessity in Latin America].

The assurance of analytical quality in a clinical laboratory is achieved through an internal system of quality control complemented by an external evaluation program. Quality assurance provides a foundation for the confidence that is placed in laboratory results and their use in the diagnosis and treatment of diseases. Many laboratories in Latin American countries do not have appropriate systems in place to evaluate and control quality. Given the importance of diagnoses based on hematologic data, the Pan American Health Organization sponsored a course in quality control in hematology during the XI Latin American Congress of Clinical Biochemistry (Mexico, 1993), in which representatives from Argentina, Chile, Cuba, Mexico, Paraguay, Dominican Republic, and Uruguay participated. As part of the course, the following control materials were produced: secondary standard solution of cyanmethemoglobin, stabilized concentrated hemoglobin solution, and preserved human whole blood with pseudoleukocytes. These materials were sent to laboratories in the seven participating countries for use in analytical procedures, and the results were then subjected to an external evaluation to assess individual performance and the comparability of results among the group. The specific tasks carried out were: (1) determination of values for hemoglobin, hematocrit, and red and white blood cell counts by the procedures normally used in each laboratory; (2) recording of the data on special reporting forms; and (3) transmittal of those forms to the coordinator in each country. The results were analyzed with regard to both the procedure used and the participating country. Reference values were established by consensus following application of a statistical method to eliminate outlying values. Comparative analysis of the results showed the coefficients of variation (CV) of the hematocrit (4.5%), red blood cell count (11.0%), and white blood cell count (22.2%) to be higher than those reported from the United States of America and Europe. With regard to analytical procedures, the manual methods yielded larger CV than the automated methods. When analysis of variance (ANOVA) was used on data broken down by country and by procedure, the only statistically significant result was for leukocyte count (P < 0.02). It was concluded that training in the preparation of quality control materials and the subsequent use of these materials in pilot surveys could provide a starting point for establishing continuous internal and external quality assessment systems in hematology. Such systems, together with continuing education for laboratory personnel and the availability of automated instrumentation, will lead to achievement of optimum laboratory quality.

Hematology↗

PubMed2006

Validation of a new technique for the quantitation of edema in the experimental setting.

BACKGROUND: An inherent limitation to the study of in vivo animal models of lymphedema is the potential inaccuracy or unreliability of existing methods for the quantification of edema volume as a surrogate functional measure of lymphatic transport capacity. Circumference-based techniques have been proposed and validated as a suitable alternative to volume displacement measurements in human clinical studies; accordingly, we have elaborated a new application of this approach that can be applied to small animal studies. METHODS: Acute postsurgical lymphedema was created experimentally in the murine tail. Both normal and lymphedematous murine tails were examined. Tail volume was quantitated both by water displacement and by a digital photographic technique. In selected mice, after sacrificed on postsurgical day 7, a 6 cm segment was resected from the midportion of the tail and cauterized to create a closed space. Known incremental volumes of saline (20-100 microL) were injected for subsequent digital photographic volumetry. RESULTS: The coefficients of variation for volume assessment by water displacement and by digital imaging were 0.08+/-0.09 and 0.01+/-0.009, respectively. The two techniques were poorly correlated: while serial water displacement analysis yielded highly variable measurements within the same tail, concurrent digital imaging of the tail circumference was quite reproducible. Furthermore, after parenteral injection of known incremental volumes of saline, the correlation between the injectate volumes and the digitally measured increases in volume was high, both in the normal and the lymphedematous tail. CONCLUSION: In the murine tail, when compared to water displacement volumetry, digital photography yields highly reproducible data. We can conclude that the lack of correlation between the two methods, with the relatively flat slope of the linear regression relationship, reflects inherent inaccuracies of the water displacement method.

Animals↗

PubMed2000

Back to the roots of a new exon--the molecular archaeology of a SP100 splice variant.

Retropseudogenes are intronless DNA sequences sharing a high degree of homology with the cDNA of their corresponding active genes. They are thought to have originated by reverse transcription of messenger RNA and reintegration of the cDNA into the genome. Usually considered a type of evolutionary waste, they melt into the background of their surrounding DNA by the loss of similarity to the active gene or disappear from the genome by the accumulation of deletions. On the other hand, in this paper we describe the evolutionary recycling of this genomic waste. Recently, a splice variant of the gene encoding the nuclear protein SP100 was identified in which the 3' part of the cDNA is replaced by an alternative exon apparently encoding an HMG1-DNA-binding domain. We were able to show that this HMG box is contributed by a new exon arising from an HMG1 retropseudogene that we have molecularly characterized in detail. In addition to being found in human cells, corresponding fusion transcripts were shown in Pan troglodytes, Gorilla gorilla, and Hylobates lar, but not in Macaca mulatta. Genomic DNA from M. mulatta enabled us to amplify by PCR the 5' part but not the 3' part of the HMG1 retropseudogene. From our data we thus can date the underlying retrotransposition to more than 35 million years ago. Our findings offer a model as to how new exons may evolve during evolution. To our knowledge this is the first example of a retropseudogene becoming part of an active gene in which both parental parts are well characterized and remain in-frame with their cDNA.

Alternative Splicing↗

PubMed2006

Locomotor behavior and long bone morphology in individual free-ranging chimpanzees.

We combine structural limb data and behavioral data for free-ranging chimpanzees from Taï (Ivory Coast) and Mahale National Parks (Tanzania) to begin to consider the relationship between individual variation in locomotor activity and morphology. Femoral and humeral cross sections of ten individuals were acquired via computed tomography. Locomotor profiles of seven individuals were constructed from 3387 instantaneous time-point observations (87.4 hours). Within the limited number of suitable chimpanzees, individual variation in locomotor profiles displayed neither clear nor consistent trends with diaphyseal cross-sectional shapes. The percentages of specific locomotor modes did not relate well to diaphyseal shapes since neither infrequent nor frequent locomotor modes varied consistently with shapes. The percentage of arboreal locomotion, rather than estimated body mass, apparently had comparatively greater biological relevance to variation in diaphyseal shape. The mechanical consequences of locomotor modes on femoral and humeral diaphyseal shapes (e.g., orientation of bending strains) may overlap between naturalistic modes more than currently is recognized. Alternatively, diaphyseal shape may be unresponsive to mechanical demands of these specific locomotor modes. More data are needed in order to discern between these possibilities. Increasing the sample to include additional free-ranging chimpanzees, or primates in general, as well as devoting more attention to the mechanics of a greater variety of naturalistic locomotor modes would be fruitful to understanding the behavioral basis of diaphyseal shapes.

Anatomy, Cross-Sectional↗

PubMed1996

The region coding for the helix termination motif and the adjacent intron 6 of the human type I hair keratin gene hHa2 contains three natural, closely spaced polymorphic sites.

Mutations in distinct sites of epidermal keratins, in particular in the helix initiation and termination regions, cause human genodermatoses due to faulty intermediate filament formation. Extension of this observation to human hereditary hair and nail diseases includes population analyses of human hair keratin genes for natural sequence variations in the corresponding sites. Here we report on a large-scale genotyping of the short helix termination region (HTR) of the human type I cortical hair keratins hHa1, a3-I, and a3-II, and the cuticular hair keratin hHa2. We describe two polymorphic loci, P1 and P2, exclusively in the cuticular hHa2 gene, both creating dimorphic protein variants. P1 is due to a C to T mutation in a CpG element leading to a threonine to methionine substitution; P2 concerns a serine codon AGT that also occurs as an asparagine coding variant AAC. A third polymorphism, P3, is linked with a C to T point mutation located at the very beginning of intron 6. The three polymorphic sites are clustered in a 39-nucleotide sequence of the hHa2 gene. Both allelic frequency calculations in individuals of different races and pedigree studies indicate that the two-allelic hHa2 variants resulting from P1 and P2 occur ubiquitously in a ratio of about 1:1 (P1) and 2:1 (P2) respectively in our survey, and are clearly inherited as Mendelian traits. A genotype carrying both mutations simultaneously on one allele could not be detected in our sampling, and there was no association of a distinct allelic hHa2 variant with the known ethnic form variations of hairs. Sequence comparisons of the HTR of hHa2 with those of other type I hair keratins including the hHa2-ortholog from chimpanzee provide evidence that the P1- and P2-linked mutations must have occurred very early in human evolution and that the two P2-associated codon variants may be the result of two independent point mutations in an ancestral AGC serine codon. These data describe natural polymorphisms in the HTR of a member of the keratin multigene family.

Alleles↗

PubMed2001

Multiple rostral medullary nuclei can influence breathing in awake goats.

The purpose of this study was to determine the effect on breathing of neuronal dysfunction in the retrotrapezoid (RTN), facial (FN), gigantocellularis reticularis (RGN), or vestibular (VN) nuclei of adult awake goats. Microtubules were chronically implanted to induce neuronal dysfunction by microinjection of an excitatory amino acid (EAA) receptor antagonist or a neurotoxin. The EAA receptor antagonist had minimal effect on eupneic breathing, but 8--10 days after injection of the neurotoxin, 7 of 10 goats hypoventilated (arterial PCO(2) increased 3.2 +/- 0.7 Torr). Overall there were no significant (P > 0.10) effects of the EAA receptor antagonist on CO(2) sensitivity. However, for all nuclei, > or =66% of the antagonist injections altered CO(2) sensitivity by more than the normal 12.7 +/- 1.6% day-to-day variation. These changes were not uniform, inasmuch as the antagonist increased (RTN, n = 2; FN, n = 7; RGN, n = 6; VN, n = 1) or decreased (RTN, n = 2; RGN, n = 3; VN, n = 2) CO(2) sensitivity. Ten days after injection of the neurotoxin into the FN (n = 3) or RGN (n = 5), CO(2) sensitivity was also reduced. Neuronal dysfunction also did not have a uniform effect on the exercise arterial PCO(2) response, and there was no correlation between effects on CO(2) sensitivity and the exercise hyperpnea. We conclude that there is a heterogeneous population of neurons in these rostral medullary nuclei (or adjacent tissue) that can affect breathing in the awake state, possibly through chemoreception or chemoreceptor-related mechanisms.

2-Amino-5-phosphonovalerate↗

PubMed2005

[Analysis and application of SNP and haplotype in the human genome].

Single nucleotide polymorphism (SNP) is the most common type of genetic variant in human genome. Haplotype, defined as a specific set of alleles observed on a single chromosome, or a part of a chromosome,has been an integral part of human genetics for decades. The goal of the international HapMap project is to determine the common patterns of DNA sequence variation and find the Tag SNPs representing all SNPs in the human genome. Some studies demonstrated that the analyses of haplotype defined by the grouping and interaction of several variants rather than any individual SNP correlated with complex phenotypes. Here, we describe the definitions of SNPs, genotype, haplotype and some information of the HapMap project. In this review, we summarize the current three haplotype-inference methods, including Clark' method, EM algorithm and Byes approach, and the different defining methods for haplotype block, as well as the methods for choosing tag SNPs and association studies of complex diseases using haplotype. The major public SNP databases and applications of SNPs and haplotype in common complex diseases and drug response are also introduced in the paper.

Algorithms↗