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Clonality studies in sacral chordoma.
Klingler L, Trammell R, Allan DG, Butler MG, Schwartz HS
(2006) Cancer Genet Cytogenet 171: 68-71
MeSH Terms: Adult, Aged, Cell Proliferation, Chordoma, Chromosomes, Human, X, Clone Cells, DNA Methylation, DNA, Neoplasm, Female, Humans, Middle Aged, Polymerase Chain Reaction, Receptors, Androgen, Sacrum, X Chromosome Inactivation
Show Abstract · Added March 5, 2014
Chordomas are rare, slow-growing, primary malignant skeletal neoplasms. Chromosome analysis, telomere reduction and telomere activity, DNA microsatellite, and loss of heterozygosity studies have been performed on chordomas; however, the clonality status (monoclonal versus polyclonal proliferation) is unknown. The primary purpose of this study was to determine whether sacral chordoma is monoclonal or polyclonal in origin with the use of a polymorphic X-linked gene (AR; alias HUMARA) and X-chromosome inactivation studies. DNA was harvested from tumor and corresponding normal tissue from eight women (37-71 years) with chordoma. Clonality was determined using an X chromosome inactivation protocol and a polymorphic human androgen receptor gene (AR) located on the X chromosome. The procedure required a methylation-specific polymerase chain reaction (PCR) and determination of the ratio of active to inactive X chromosomes. Results were informative for seven of the eight women, with two separate X-linked alleles seen for the AR gene in the normal tissue. Expression of AR gene alleles from each of the two X chromosomes was present in the chordoma tumor, indicating a polyclonal proliferation in all seven women. Most solid tumors and skeletal neoplasms are polyclonal in nature. Our study indicates that chordoma is polyclonal in its pattern of proliferation.
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15 MeSH Terms
Genetic linkage of human height is confirmed to 9q22 and Xq24.
Liu YZ, Xiao P, Guo YF, Xiong DH, Zhao LJ, Shen H, Liu YJ, Dvornyk V, Long JR, Deng HY, Li JL, Recker RR, Deng HW
(2006) Hum Genet 119: 295-304
MeSH Terms: Adult, Aged, Body Height, Chromosome Mapping, Chromosomes, Human, Pair 9, Chromosomes, Human, X, Family, Female, Genetic Linkage, Humans, Inheritance Patterns, Lod Score, Male, Middle Aged, Quantitative Trait Loci
Show Abstract · Added December 10, 2013
Human height is an important and heritable trait. Our previous two genome-wide linkage studies using 630 (WG1 study) and an extended sample of 1,816 Caucasians (WG2 study) identified 9q22 [maximum LOD score (MLS)=2.74 in the WG2 study] and preliminarily confirmed Xq24 (two-point LOD score=1.91 in the WG1 study, 2.64 in the WG2 study) linked to height. Here, with a much further extended large sample containing 3,726 Caucasians, we performed a new genome-wide linkage scan and confirmed, in high significance, the two regions' linkage to height. An MLS of 4.34 was detected on 9q22 and a two-point LOD score of 5.63 was attained for Xq24. In an independent sub-sample (i.e., the subjects not involved in the WG1 and WG2 studies), the two regions also achieved significant empirical P values (0.002 and 0.004, respectively) for "region-wise" linkage confirmation. Importantly, the two regions were replicated on a genotyping platform different from the WG1 and WG2 studies (i.e., a different set of markers and different genotyping instruments). Interestingly, 9q22 harbors the ROR2 gene, which is required for growth plate development, and Xq24 was linked to short stature. With the largest sample from a single population of the same ethnicity in the field of linkage studies for complex traits, our current study, together with two previous ones, provided overwhelming evidence substantiating 9q22 and Xq24 for height variation. In particular, our three consecutive whole genome studies are uniquely valuable as they represent the first practical (rather than simulated) example of how significant increase in sample size may improve linkage detection for human complex traits.
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Mapping quantitative trait loci for cross-sectional geometry at the femoral neck.
Shen H, Long JR, Xiong DH, Liu YJ, Liu YZ, Xiao P, Zhao LJ, Dvornyk V, Zhang YY, Rocha-Sanchez S, Liu PY, Li JL, Deng HW
(2005) J Bone Miner Res 20: 1973-82
MeSH Terms: Absorptiometry, Photon, Adult, Age Factors, Aged, Aged, 80 and over, Bone Density, Chromosomes, Human, Pair 10, Chromosomes, Human, Pair 20, Chromosomes, Human, X, European Continental Ancestry Group, Female, Femur Neck, Genetic Linkage, Genome, Human, Humans, Lod Score, Male, Microsatellite Repeats, Middle Aged, Pedigree, Principal Component Analysis, Quantitative Trait Loci, Sex Factors
Show Abstract · Added December 10, 2013
UNLABELLED - A genome-wide linkage scan was performed in a sample of 79 multiplex pedigrees to identify genomic regions linked to femoral neck cross-sectional geometry. Potential quantitative trait loci were detected at several genomic regions, such as 10q26, 20p12-q12, and chromosome X.
INTRODUCTION - Bone geometry is an important determinant of bone strength and osteoporotic fractures. Previous studies have shown that femoral neck cross-sectional geometric variables are under genetic controls. To identify genetic loci underlying variation in femoral neck cross-sectional geometry, we conducted a whole genome linkage scan for four femoral neck cross-sectional geometric variables in 79 multiplex white pedigrees.
MATERIALS AND METHODS - A total of 1816 subjects from 79 pedigrees were genotyped with 451 microsatellite markers across the human genome. We performed linkage analyses on the entire data, as well as on men and women separately.
RESULTS - Significant linkage evidence was identified at 10q26 for buckling ratio (LOD = 3.27) and Xp11 (LOD = 3.45) for cortical thickness. Chromosome region 20p12-q12 showed suggestive linkage with cross-sectional area (LOD = 2.33), cortical thickness (LOD = 2.09), and buckling ratio (LOD = 1.94). Sex-specific linkage analyses further supported the importance of 20p12-q12 for cortical thickness (LOD = 2.74 in females and LOD = 1.88 in males) and buckling ratio (LOD = 5.00 in females and LOD = 3.18 in males).
CONCLUSIONS - This study is the first genome-wide linkage scan searching for quantitative trait loci underlying femoral neck cross-sectional geometry in humans. The identification of the genes responsible for bone geometric variation will improve our knowledge of bone strength and aid in development of diagnostic approaches and interventions for osteoporotic fractures.
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23 MeSH Terms
Genetic dissection of human stature in a large sample of multiplex pedigrees.
Liu YZ, Xu FH, Shen H, Liu YJ, Zhao LJ, Long JR, Zhang YY, Xiao P, Xiong DH, Dvornyk V, Li JL, Conway T, Davies KM, Recker RR, Deng HW
(2004) Ann Hum Genet 68: 472-88
MeSH Terms: Adult, Aged, Body Height, Chromosome Mapping, Chromosomes, Human, X, European Continental Ancestry Group, Female, Genetic Linkage, Genomics, Genotype, Humans, Male, Middle Aged, Pedigree, Reference Values
Show Abstract · Added December 10, 2013
Recently, we reported a whole genome scan on a sample of 630 Caucasian subjects from 53 human pedigrees. Several genomic regions were suggested to be linked to height. In an attempt to confirm the identified genomic regions, as well as to identify new genomic regions linked to height, we conducted a whole genome linkage study on an extended sample of 1,816 subjects from 79 pedigrees, which includes the 53 pedigrees containing the original 630 subjects from our previous whole genome study and an additional 128 new subjects, and 26 further pedigrees containing 1,058 subjects. Several regions achieved suggestive linkage signals, such as 9q22.32 [MLS (multipoint LOD score) = 2.74], 9q34.3 [MLS = 2.66], Xq24 [two-point LOD score = 2.64 at the marker DXS8067], and 7p14.2 [MLS = 2.05]. The importance of the above regions is supported either by other whole genome studies or by candidate genes within these regions relevant to linear growth or pathogenesis of short stature. In addition, this study has tentatively confirmed the Xq24 region's linkage to height, as this region was also detected in the previous whole genome study. To date, our study has achieved the largest sample size in the field of genetic linkage studies of human height. Together with the findings of other studies, the current study has further delineated the genetic basis of human stature.
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15 MeSH Terms
A genome-wide linkage scan for bone mineral density in an extended sample: evidence for linkage on 11q23 and Xq27.
Shen H, Zhang YY, Long JR, Xu FH, Liu YZ, Xiao P, Zhao LJ, Xiong DH, Liu YJ, Dvornyk V, Rocha-Sanchez S, Liu PY, Li JL, Conway T, Davies KM, Recker RR, Deng HW
(2004) J Med Genet 41: 743-51
MeSH Terms: Bone Density, Chromosomes, Human, Pair 11, Chromosomes, Human, X, Female, Genetic Linkage, Genome, Human, Genomics, Genotype, Humans, Lod Score, Male, Middle Aged, Pedigree
Show Abstract · Added December 10, 2013
BACKGROUND - Osteoporosis is a major public health problem, mainly quantified by low bone mineral density (BMD). The majority of BMD variation is determined by genetic effects. A pilot whole genome linkage scan (WGS) was previously reported in 53 white pedigrees with 630 subjects. Several genomic regions were suggested to be linked to BMD variation.
OBJECTIVE - To substantiate these previous findings and detect new genomic regions.
METHODS - A WGS was conducted on an extended sample where the size was almost tripled (1816 subjects from 79 pedigrees). All the subjects were genotyped with 451 microsatellite markers spaced approximately 8.1 cM apart across the human genome. Two point and multipoint linkage analyses were carried out using the variance component method.
RESULTS - The strongest linkage signal was obtained on Xq27 with two point LOD scores of 4.30 for wrist BMD, and 2.57 for hip BMD, respectively. Another important region was 11q23, which achieved a maximum LOD score of 3.13 for spine BMD in multipoint analyses, confirming the results on this region in two earlier independent studies. Suggestive linkage evidence was also found on 7p14 and 20p12.
CONCLUSIONS - Together with the findings from other studies, the current study has further delineated the genetic basis of bone mass and highlights the importance of increasing sample size to confirm linkage findings and to identify new regions of linkage.
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13 MeSH Terms
Comparative sequence and x-inactivation analyses of a domain of escape in human xp11.2 and the conserved segment in mouse.
Tsuchiya KD, Greally JM, Yi Y, Noel KP, Truong JP, Disteche CM
(2004) Genome Res 14: 1275-84
MeSH Terms: Actins, Animals, CHO Cells, Cell Line, Chromosome Mapping, Chromosomes, Human, X, Conserved Sequence, Cricetinae, Dosage Compensation, Genetic, Expressed Sequence Tags, Genes, Humans, Interspersed Repetitive Sequences, Long Interspersed Nucleotide Elements, Male, Mice, Molecular Sequence Data, Organ Specificity, Pseudogenes, Sequence Homology, Nucleic Acid, Transcription, Genetic, X Chromosome
Show Abstract · Added March 5, 2014
We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared this region with the region of conserved synteny in mouse. We identified several new transcripts from this region in human and in mouse, which defined the full extent of the domain escaping X inactivation in both species. In human, escape from X inactivation involves an uninterrupted 235-kb domain of multiple genes. Despite highly conserved gene content and order between the two species, Smcx is the only mouse gene from the conserved segment that escapes inactivation. As repetitive sequences are believed to facilitate spreading of X inactivation along the chromosome, we compared the repetitive sequence composition of this region between the two species. We found that long terminal repeats (LTRs) were decreased in the human domain of escape, but not in the majority of the conserved mouse region adjacent to Smcx in which genes were subject to X inactivation, suggesting that these repeats might be excluded from escape domains to prevent spreading of silencing. Our findings indicate that genomic context, as well as gene-specific regulatory elements, interact to determine expression of a gene from the inactive X-chromosome.
Copyright 2004 Cold Spring Harbor Laboratory Press ISSN
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22 MeSH Terms
Fatal hemophagocytic lymphohistiocytosis associated with Epstein-Barr virus infection in a patient with a novel mutation in the signaling lymphocytic activation molecule-associated protein.
Halasa NB, Whitlock JA, McCurley TL, Smith JA, Zhu Q, Ochs H, Dermody TS, Crowe JE
(2003) Clin Infect Dis 37: e136-41
MeSH Terms: Adolescent, Carrier Proteins, Chromosomes, Human, X, Epstein-Barr Virus Infections, Herpesvirus 4, Human, Histiocytosis, Non-Langerhans-Cell, Humans, Intracellular Signaling Peptides and Proteins, Male, Mutation, Proline, Serine, Signaling Lymphocytic Activation Molecule Associated Protein
Show Abstract · Added December 10, 2013
Individuals with X-linked lymphoproliferative disease are susceptible to severe Epstein-Barr virus (EBV) infections that are often fatal. Mutations in signaling lymphocytic activation molecule-associated protein (SAP) are associated with this illness. We describe a patient with a novel serine-to-proline mutation at aa 57 in SAP and compare the location of the altered amino acid with all known missense mutations in the SAP-encoding SH2D1A gene, including those of 4 additional individuals whose cases have not been described elsewhere. The patient's genetic condition was discovered only after he exhibited an abnormal host response to primary EBV infection that resulted in hemophagocytic lymphohistiocytosis syndrome, which was complicated by marrow aplasia with terminal disseminated aspergillosis.
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13 MeSH Terms