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PubMed2006

Immunohistochemical and genetic analysis of Chinese nasal natural killer/T-cell lymphomas.

Nasal natural killer/T-cell lymphoma (N-NK/T-L) is prevalent in China. To further characterize this neoplasm, 36 cases of N-NK/T-L from 304 cases of malignant lymphomas in the north China area were investigated by histopathology, immunophenotyping, and genomic analysis of c-kit, in comparison with 11 cases of B-cell lymphoma (BCL) at the same region and 5 cases of nodal peripheral T-cell lymphoma (PTCL) (unspecified). Histopathologically, N-NK/T-L was characterized by coagulative necrosis, inflammatory background, and angiodestructive growth pattern. In 36 cases of N-NK/T-L, 27 cases (75.0%) were stained for CD45RO and 25 (72.2%) for CD3epsilon. Thirty cases (83.3%) were positive for T-cell intracellular antigen-1, 22 (61.1%) for granzyme B, 18 (50.0%) for CD56, and 11 (30.6%) for CD30, whereas none was positive for CD117. All 5 cases of PTCL displayed positive staining for CD45RO and T-cell intracellular antigen-1, 3 cases for CD3epsilon, but only 1 case for granzyme B. All 11 BCLs presented positive staining for CD20 and CD79a but negative for other antibodies. A significant relationship was observed between neoplastic cells pleomorphism and granzyme B expression (P < .05). Despite the fact that all cases were negative for CD117 staining, genomic sequences of c-kit 11 and exon 17 sequencing showed that 8 (26%) of 31 cases N-NK/T-L proved to contain genomic mutations, including 4 cases in exon 11 and 4 in exon 17. For the control group, only 1 (9%) of 11 BCLs and 1 (20%) of 5 cases of PTCL were detected to harbor mutations in exon 11. All mutations detected in 3 groups were missense by base substitution, and codes 571, 572, and 821 were hot spots. The results suggested that, in addition to histological features and routine immunophenotyping, granzyme B expression should be a more reliable marker in correct diagnosis of N-NK/T-L, and genetic analysis of c-kit mutation should be helpful in the diagnosis of this tumor.

Adolescent↗
PubMed2004

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

Databases, Genetic↗
PubMed2006

Ectrodactyly with aplasia of long bones (OMIM; 119100) in a large inbred Arab family with an apparent autosomal dominant inheritance and reduced penetrance: clinical and genetic analysis.

Ectrodactyly with aplasia of long bones syndrome is one of the most recognizable defects involving the extremities. We have studied a very large eight-generation consanguineous Arab family from the United Arab Emirates (UAE) with multiple severe limb anomalies resembling this condition (OMIM; 119100), for which the affected gene is unknown. The pedigree consists of 145 individuals including 23 affected (14 males/9 females) with limb anomalies. Of these, 18 had tibial aplasia (TA) usually on the right side. The expression of the phenotype was variable and ranged from bilateral to unilateral TA with ectrodactyly and other defects of the extremities. The mode of inheritance appears to be autosomal dominant with reduced penetrance. There were 10 consanguineous marriages observed in this pedigree. This could suggest possible pseudodominance due to high frequency of the mutant allele. Candidate loci for the described syndrome include GLI3 (OMIM: 165240) on 7p13, sonic hedgehog; (OMIM: 600725) on 7q36, Langer-Giedion syndrome (OMIM: 150230) on 8q24.1 and split-hand/foot malformation 3 (OMIM: 600095) on 10q24. In addition, bilateral tibial hemimelia and unilateral absence of the ulna was previously observed to co-segregate with deletion of 8q24.1. Two-point linkage and haplotype analyses did not show the involvement of the above regions in this family.

Abnormalities, Multiple↗
PubMed2006

Genetic analysis of the diabetes-prone C57BLKS/J mouse strain reveals genetic contribution from multiple strains.

The C57BLKS/J (BKS) inbred mouse strain is a widely used animal model of type 2 diabetes. In the presence of the diabetes (db) mutation, obese BKS-db mice develop severe diabetes. Genetic studies of diabetes-susceptibility in this strain are facilitated by the fact that BKS is a genetic composite between the diabetes-resistant C57BL/6J (B6) and susceptible DBA/2J (DBA) strains. On this basis, it has been hypothesized that diabetes-susceptibility in BKS is conferred by DBA-derived alleles. However, recent studies revealed non-B6/non-DBA genetic material in BKS. To identify the origin of this genetic component, we generated a genomic map of BKS using 537 microsatellite markers. Our results demonstrate that, in addition to B6 and DBA, BKS contains alleles from at least three other strains, including 129, C57BL/10 and an unidentified mouse strain. We also analyzed two congenic strains, B6-db and BKS-db, which are widely used for the genetic mapping of diabetes-susceptibility loci. We identified several donor-derived genomic regions introduced during the generation of these congenic strains. In summary, our study reveals novel aspects of the genetic fine-structure of BKS and related strains and facilitates the identification of diabetes-susceptibility loci in this mouse model.

Alleles↗
PubMed2006

Genetic analysis of oil content in Brassica napus L. using mixed model of major gene and polygene.

The joint segregation analysis of a mixed genetic model of major gene plus poly-gene was conducted to study the inheritance of oil content in Brassica napus L.. Five populations, i.e the populations of 2 parents (P1 and P2), F1, F2 and F2:3 (derived from F2) family, from each of the two crosses (1141B x Ken C-1, 32B x Ken C1-2) were investigated.The frequency distributions of oil content in F2 and F2:3 family populations show characteristics of a mixed normal distribution, which indicated that the inheritance of oil content followed a major gene plus poly-gene model. Twenty-one genetic models were established, which could be classified into five types: one and two major genes, polygenes, one and two major genes plus polygenes. The most suitable genetic model could be selected using Akaike's Information Criterion and the fitness of the selected one could be examined by a set of tests. Results show that genetic model D-2 is the most fitting genetic model for the trait. In other words, oil content in oilseed rape is controlled by one additive major gene plus additive and dominance polygenes. For cross 1 (1141B x Ken C1-1) the heritabilities of major gene and poly-genes in F2 are 68.21% and 27.17%, respectively, and in F2:3 are 81.70% and 16.80%, respectively. The additive effect of major gene is -1.74, which indicates that the locus of the allele in parent 1141B may decrease the oil content, but that in parent Ken C1-1 may increase it. The additive and dominance effects of the polygenes are 1.20 and -1.93, respectively. For cross 2 (32B x Ken C1-2) the heritabilities of major gene and polygenes in F2 are 66.20% and 28.10%, respectively, and in F2:3 were 81.00% and 14.90%, respectively. The additive effect of major gene was -3.74, which also indicates that the locus of the allele in parent 32B may decrease the oil content, but that in parent Ken C1-2 may increase it. The additive and dominance effects are -1.99 and 0.93, respectively. The heritability of the major gene in F2:3 is higher than that in F2 in both crosses, so it would be more efficent to conduct selection in F2:3 families for high oil content in breeding.

Brassica napus↗
PubMed2001

Genetic analysis of a selection experiment on the growth curve of chickens.

A selection experiment on the shape of the growth curve was performed on meat-type chickens through combined selection on juvenile and adult BW. Line X-+ was selected for low BW at 8 wk (BW8) and high BW at 36 wk (BW36). Line X+- was selected for high BW8 and low BW36. Line X++ was selected for high BW8 and BW36, and X-- was selected for low BW8 and BW36. Line X00 was maintained as an unselected control. Data on the first 14 generations (i.e., 38,693 birds) were used. The growth curve was modeled using a Gompertz function on 7,143 birds that were weighed regularly. Selection for higher BW8 increased BW from 4 to 16 wk, initial specific growth rate, and maturation rate and decreased age at inflection. Selection for higher BW36 resulted in increased BW36, asymptotic BW, and estimated BW at hatching. Body weights were more modified in Lines X++ and X--, but the growth curve parameters changed more in Lines X-+ and X-- than in Lines X++ and X+-.

Aging↗
PubMed2004

Extranodal follicular lymphoma: a clinicopathological and genetic analysis of 15 cases arising at non-cutaneous extranodal sites.

AIMS: Recent studies of primary cutaneous follicular lymphoma suggest that it represents a clinicopathological entity distinct from nodal follicular lymphoma (FL). The purpose of this study was to determine if FL arising at other extranodal sites is more closely related to FL occurring in the skin or in lymph nodes. METHODS AND RESULTS: Fifteen cases of non-cutaneous extranodal follicular lymphoma (ENFL) were identified from the Scotland and Newcastle Lymphoma Group (SNLG) database. All were stage 1E at presentation and involved the tonsil (n = 3), palate (n = 3), skeletal muscle (n = 2), ileum (n = 2), duodenum (n = 1), stomach (n = 1), thyroid gland (n = 1), submandibular gland (n = 1) and fallopian tube (n = 1). Polymerase chain reaction for t(14;18) using primers to the major breakpoint cluster region was performed on 14 cases of ENFL and the incidence of the translocation compared with that found in 16 cases of stage 1 nodal FL. Clinical and follow-up data were obtained from the SNLG database for the 15 cases of ENFL and 87 cases of stage 1 nodal FL, and a comparison of outcomes made. Only 2/14 cases of ENFL had detectable t(14;18) compared with 9/16 stage 1 nodal FL (P < 0.01). Freedom from progression and disease-specific survival was similar for the 15 cases of ENFL and 87 cases of stage 1 nodal FL. However, 13/15 patients with ENFL were disease free at the end of follow-up compared with 49/87 stage 1 nodal FL (P < 0.02). CONCLUSIONS: The low incidence of t(14;18) and favourable outcome encountered in ENFL in this study is similar to that previously found for primary cutaneous FL. These results support the concept of a subtype of FL lacking t(14;18) involving the major breakpoint cluster region, and with a propensity to arise at extranodal sites. Despite a high relapse rate, patients with ENFL are more likely to achieve complete remission and may ultimately have a more favourable long-term prognosis than those with equivalent nodal disease.

Adult↗
PubMed1983

Genetic analysis of the proBA genes of Salmonella typhimurium: physical and genetic analyses of the cloned proB+ A+ genes of Escherichia coli and of a mutant allele that confers proline overproduction and enhanced osmotolerance.

Because of the fact that proline overproduction relieves the inhibitory effects of high external osmotic strength in a number of procaryotes, we wished to clone a mutant allele, pro-74, that confers proline overproduction and enhanced osmotolerance on Salmonella typhimurium and Escherichia coli. Therefore, the pro-74 allele, originally located on an E. coli episome F'128, was cloned into pBR322. In a parallel experiment, the wild type proB+ A+ genes of E. coli were also cloned from F'128 into pBR322. Both the pro-74 and the proB+ A+ alleles were obtained on a 10.4-kilobase-pair fragment that also contained the unrelated phoE gene. Strains carrying either the wild-type proB+ A+ or the pro-74 alleles on pBR322 grew more slowly, both in minimal medium and media of elevated osmotic strength, than strains carrying the same alleles on the low-copy plasmid, F'128, indicating that some gene in the cloned region is deleterious in high copy. We constructed Tn5 insertion mutations in the proB and the proA genes of E. coli, carried on F'128 in S. typhimurium. Using P22 transduction in S. typhimurium, we transferred these proB and proA::Tn5 insertions from F'128 into the cloned proBA genes on pBR322. From the restriction maps of the plasmids thus generated, we determined the approximate locations of the proB and the proA genes. We also performed complementation tests of S. typhimurium and E. coli proB and proA mutants by using the F'128 proB and proA::Tn5 insertions. These tests revealed that the proBA genes of S. typhimurium form an operon, whose direction of transcription is from proB to proA. They also indicated that in S. typhimurium, as in E. coli, the proB+ gene encodes gamma-glutamyl kinase, and the proA+ gene encodes gamma-glutamyl phosphate reductase. Complementation tests also indicated that the pro-74 mutation is either in the proB structural gene, or its promoter-operator.

Aldehyde Oxidoreductases↗
PubMed1998

Nucleotide sequence and genetic analysis of the leader region of Canadian, American and European equine arteritis virus isolates.

The extreme 5' end, the entire leader sequence of the Arvac vaccine strain, and 10 equine arteritis virus (EAV) isolates, including the ATCC Bucyrus reference strain and 5 Canadian field isolates, were determined and compared at the primary nucleotide and secondary structure levels. The leader sequence of eight EAV isolates, including the Bucyrus reference strain, and the leader sequence of the Arvac vaccine strain was determined to be 206 nt in length (not including the putative 5' cap structure-associated nucleotide) whereas those of the 86AB-A1 and 86NY-A1 isolates were found to be 205 and 207 nt in length, respectively. The sequence identity of the leader sequences, between the different isolates and the Bucyrus reference strain, ranged from 94.2 to 98.5%. Phylogenetic analysis and estimation of genetic distances, based on the leader nucleic acid sequences, showed that all EAV isolates/strains are likely to represent a large phylogenetically-related group. An AUG start codon found at position 14 in all EAV isolates/strains could initiate an open reading frame (ORF) that could produce a polypeptide of 37 amino acids, except for the 86NY-A1 isolate where the intraleader polypeptide would contain 54 amino acids. Computer-predicted RNA secondary structures were identified in the 11 EAV leader regions analyzed. All EAV isolates/strains showed 3 conserved stem-loops (designated A, B and C). An additional conserved stem-loop (D) was observed in 7 EAV isolates, including the Bucyrus reference strain. The leader region distal to stem-loop D did not contain conserved sequences or stem-loop structures common to the EAV isolates/strains.

Animals↗
PubMed2004

Genetic analysis of human H2N2 and early H3N2 influenza viruses, 1957-1972: evidence for genetic divergence and multiple reassortment events.

Phylogenic analysis of all gene segments of human H2N2 viruses isolated from 1957 to 1968 was undertaken to better understand the evolution of this virus subtype. Human H3N2 viruses isolated from 1968 to 1972 were also examined to investigate genetic events associated with their emergence in humans and to identify the putative H2N2 ancestral virus. All gene segments of human H2N2 viruses demonstrated divergent evolution into two distinct clades (I and II) among late H2N2 isolates. All gene segments of 1968 H3N2 viruses that were retained from human H2N2 viruses were most similar to clade I H2N2 genes. However, genes of both clades were found among H3N2 isolates of 1969-1971. Unique phylogenic topologies reflected multiple reassortment events among late H2N2 or H3N2 viruses that resulted in a variety of different genome constellations. These results suggest that H2N2 viruses continued to circulate after 1968 and that establishment of H3N2 viruses in humans was associated with multiple reassortment events that contributed to their genetic diversity.

Amino Acid Sequence↗
PubMed1984

[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↗
PubMed2003

Genetic analysis of a Sicilian population using 15 short tandem repeats.

The genetic structure of the population of Alia (Sicily, Italy) was analyzed using 15 short tandem repeats: TPOX, D2S1338, D3S1358, FIBRA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D19S433, and D21S11. Two of these markers, D2S1338 and D19S433, have never before been used in research on population genetics and only recently have they been put to use in forensic medicine. Results of the analysis underline the genetic isolation of the Alia population and show it to be a recent bottleneck as a consequence of a cholera epidemic in 1837. While comparing the Alia population with other populations from Sicily, a genetic heterogeneity within Sicily was uncovered, thus confirming previous results obtained from the analysis of classical markers. This heterogeneity underlines the existence of genetic boundaries within the island. Comparisons with other Italian, Mediterranean, and European populations highlight the differentiation of the Sicilian population, reflecting the presence of a genetic boundary that separates Sicily from northern and central Italy and from the western Mediterranean basin.

Adult↗
PubMed1997

DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis.

MOTIVATION: Several methods in molecular population genetics have recently been described to estimate the amount and pattern of the DNA polymorphism in natural populations, and also to test the neutral theory of molecular evolution. These methods are essential for understanding the molecular evolutionary process. However, a comprehensive computer program for the analysis is not currently available. RESULTS: Here we present DnaSP (DNA Sequence Polymorphism) version 2.0, a software package for Windows that performs extensive population genetics analyses on DNA sequence data. DnaSP estimates several measures of DNA sequence variation within and between populations, linkage disequilibrium, recombination, gene flow and gene conversion (a new algorithm to detect gene conversion tracts has been included). DnaSP can also carry out several tests of neutrality: those of Fu and Li; Hudson, Kreitman and Aguadé; and Tajima. The results of the analyses are displayed in tabular and graphic form. AVAILABILITY: For academic uses, DnaSP is available via anonymous ftp: ftp.ebi.ac.uk in the directory/pub/software/dos.

Algorithms↗
PubMed1986

Genetic analysis of cystic fibrosis using linked DNA markers.

Genetic linkage has been analyzed between cystic fibrosis (CF) and a number of markers on the long arm of chromosome 7, including D7S15, COL1A2, PON, MET, D7S8, and TCRB, using a cohort of 47 Canadian and 13 Danish CF families. The analysis confirms the previous observations that both MET and D7S8 are closely linked to CF. Based on the result from one family, MET appears to be more proximal to the centromere than CF. Our analysis also suggests that genetic heterogeneity may account for the high recombination fraction between CF and D7S8 observed in another family. In addition, a strong linkage disequilibrium has been observed between CF and the two closely flanking markers.

Chromosomes, Human, Pair 7↗
PubMed1997

Genetic analysis of families with nonsmoking lung cancer probands.

As part of a genetic epidemiologic study of lung cancer among nonsmokers, we investigated the role of genetic predisposition in familial aggregation. Cases were identified from the Metropolitan Detroit Cancer Surveillance System. Information on lung cancer occurrence, smoking habits (active or passive), and chronic respiratory diseases in first-degree relatives was obtained for 257 nonsmoking lung cancer probands (71 males, 186 females) diagnosed at ages 40-84 years. Among the 2,021 first-degree relatives, 24 (2.6%) males and 10 (1.1%) females were reported as having lung cancer. The occurrence of lung cancer among smoking and nonsmoking relatives was 4.5% and 1.1% in males and 2.8% and 0.4% in females, respectively. To evaluate the role of a putative Mendelian gene (one locus, two alleles) in the presence of other risk factors, we performed complex segregation analyses on the data using two different regressive model approaches [Segregation Analysis of a Discrete Trait Under a Class A Regressive Logistic Model, V4.0 (REGD) and Segregation Analysis of a Truncated Trait, V2.0, Model 1(REGTL)] as implemented in the Statistical Analysis for Genetic Epidemiology (SAGE) program. Using either approach, an environmental model best explained the observed lung cancer aggregation in families ascertained through nonsmoking probands. Based on our final model, only 0.04% of this population had a very high risk and 4.2% had a moderate risk of lung cancer. The rest of the population had virtually no risk of lung cancer during their lifetime unless they have multiple risk factors. Among the high-risk individuals without any risk factor under study, the estimated risks at ages 40, 60, and 80 years in males were 16.7%, 83.6%, and 95.4%, and in females were 14.0%, 72.2%, and 88.0%, respectively. Among at-moderate-risk smokers the estimated risks at the same age and gender groups were essentially the same as in the high-risk nonsmokers. Our results suggest that the pattern of lung cancer occurrence in families of nonsmoking lung cancer patients differs from that in families of smoking lung cancer patients. Despite the profound effect of smoking on the risk of lung cancer, other environmental and/or genetic risk factors need to be identified.

Adult↗
PubMed2005

Informed consent, participation in, and withdrawal from a population based cohort study involving genetic analysis.

OBJECTIVE: Population based cohort studies involving genetic research have been initiated in several countries. However, research published to date provides little information on the willingness of the general population to participate in such studies. Furthermore, there is a need to discover the optimal methods for acquiring fully informed consent from the general population. We therefore examined the results of a population based genetic cohort study to identify the factors affecting the participation rate by members of the general public and also specifically to examine the impact of different consent procedures on the rate of participation by prospective candidates and their subsequent withdrawal rate from the study. DESIGN: Descriptive analyses. SETTING AND PARTICIPANTS: The study evaluated two non-genetic subcohorts comprising 3166 people attending for a health checkup during 2002, and two genetic subcohorts comprising 2195 people who underwent a checkup during 2003. MAIN OUTCOME MEASUREMENTS: Analysis endpoints were differences in participation rates between the non-genetic and genetic subcohorts, differences between providing non-extensive and extensive preliminary information, and changes in participation status between baseline and at 6 months. RESULTS: Participation rates in the genetic subcohorts were 4.7-9.3% lower than those in the non-genetic subcohorts. The odds ratios (OR) of participation in genetic research were between 0.60 and 0.77, and the OR for withdrawal from the research was over 7.70; providing preliminary extensive information about genetic research reduced the withdrawal risks (OR 0.15 for all dependent variables) but worsened participation rates (OR 0.63-0.74). CONCLUSIONS: The general population responded sceptically towards genetic research. It is crucial that genetic researchers utilise an informative and educational consent process worthy of public trust.

Adolescent↗