Structure and location of the murine adrenoleukodystrophy gene

X-linked adrenoleukodystrophy (ALD) is a degenerative neurological disease characterized by the accumulation of very long chain fatty acids in various tissues and demyelination of the central nervous system. The human gene responsible for the disease encodes a membrane-bound ATP-binding transporter protein that is located in peroxisomes. We isolated the mouse adrenoleukodystrophy gene, determined its structure, and mapped it both cytogenetically and genetically. The mouse gene is very similar in structure to the human gene, consisting of 10 exons arranged over a 22-kb genomic region. We localized it in band B of the mouse X chromosome by fluorescence in situ hybridization analysis and, using a new microsatellite repeat polymorphism, determined the map location as 47 cM from the X centromere. We found evidence for other sequences in the mouse genome related to the 3' end of Aldgh. This study paves the way for the construction of gene-targeting plasmids that may be used to develop an animal model of ALD.

Physical mapping of 49 microsatellite markers on chromosome 19 and correlation with the genetic linkage map

We have regionally localized 49 microsatellite markers developed by Généthon using a panel of previously characterized somatic cell hybrids that retain fragments from chromosome 19. The tight correlation observed between the physical and the genetic orders of the microsatellites provide cytogenetic anchorages to the genetic map data. We propose a position for the centromere just above D19S415, from the study of two hybrids, each of which retains one of the two derivatives of a balanced translocation t(1;19)(q11;q11). Microsatellites, which can be identified by a standard PCR protocol, are useful tools for the localization of disease genes and for the establishment of YAC or cosmid contigs. These markers can also judiciously be used for the characterization of new hybrid cell line panels. We report such a characterization of 11 clones, 8 of which were obtained by irradiation-fusion. Using the whole hybrid panel, we were able to define the order of 12 pairs of genetically colocalized microsatellites. As examples of gene mapping by the combined use of microsatellites and hybrid cell lines, we regionally assigned the PVS locus between the 19q13.2 markers D19S417 and D19S423 and confirmed the locations of fucosyltransferase loci FUT1, FUT2, and FUT5.

Microsatellite instability, apoptosis, and loss of p53 function in drug-resistant tumor cells

We have examined microsatellite instability and loss of p53 function in human tumor cell line models of acquired anticancer drug resistance. We observe acquisition of an RER(+) phenotype in cell lines selected for resistance to cisplatin or doxorubicin. The majority of independent cisplatin-resistant sublines are RER(+), whereas the parental line shows no evidence of microsatellite instability. Microsatellite mutations in random, nonselected subclones of a cislatin-resistant line are observed in the absence of further drug exposure, suggesting that the RER(+) phenotype is a stable phenotype rather than being transiently induced by DNA damage. Furthermore, a cisplatin-resistant derivative shows reduction in a G:T mismatch recognition activity compared to the parental line. Independent lines selected by multiple exposure to cisplatin show resistance factors of up to a 5-fold by clonogenic assay and have reduced cisplatin-induced apoptosis. The resistant lines that are RER(+) show evidence of loss of p53-dependent functions, as measured by a loss of radiation-induced G(1) arrest and reduced CIP1 mRNA. Induced loss of p53 function by transfection of mutant TP53 does not cause a detectable RER(+) phenotype. We speculate that tolerance of DNA damage and expansion of cells with an RER(+) phenotype may select for reduced ability to engage apoptosis and loss of p53 function.

Microsatellite instability in nonneoplastic mucosa from patients with chronic ulcerative colitis

Microsatellite instability (MIN) has been detected in many cancer types; however, recently we also observed it in the nonneoplastic but inflammatory setting of pancreatitis. Consequently, we sought to examine whether MIN was present in another inflammatory condition, ulcerative colitis (UC). MIN was found in 50% of UC patients whose colonic mucosa was negative for dysplasia, 46% of those with high-grade dysplasia, and 40% of those with cancer but in none of the ischemic or infectious colitis controls (P<0.03). Thus, UC patients may have MIN within mucosa that has no histological evidence of neoplastic change. MIN in this setting may reflect the inability of DNA repair mechanisms to compensate for the stress of chronic inflammation, and may be one mechanism for the heightened neoplastic risk in UC.

Microsatellite instability in human atherosclerotic plaques

The aetiopathology of atherosclerosis remains obscure. Although histologically the accumulation of lipids and the proliferation of the smooth muscle cells represents the main feature of the disease, little is known as regards the molecular alterations associated with the atherosclerotic lesions. In the present study we investigated whether an elevated mutational rate is detectable in human atheromatous plaques. Thirty specimens were assessed for microsatellite instability (MI) by 7 microsatellite markers and MI, in at least one marker, was apparent in 6 (20%) cases. Our data suggest that decreased fidelity in DNA replication and repair may be associated with the development of the disease.

Molecular analysis of a RAPD marker (B20) reveals two microsatellites and differential mRNA expression in Penaeus vannamei

We previously reported a population-specific DNA fragment (B20) in Penaeus vannamei shrimp, fragment found using the randomly amplified polymorphic DNA (RAPD) procedure, that was present in Population 2 but not in Populations 1 and 4. The specific objectives of this study were to clone and sequence this genetic marker, determine if all or part of this cloned sequence could be found in any of the other populations in which this marker could not be amplified, and examine if this marker represents a functional gene by examining the steady-state levels of mRNA expression using Northern blot hybridization. Sequence information of the 1259-bp B20 clone revealed two microsatellites and two candidate open reading frames. Although the entire B20 sequence could only be amplified in Population 2 (from Ecuador), Population 3 (a hybrid of Populations 1 and 2), and a few individuals from wild Ecuadorian shrimp samples, portions of the B20 DNA could be amplified in individuals from Populations 1, 2, 3, candidate Population 4, and wild Ecuadorian samples. These microsatellites vary in size between populations and families. Northern blot hybridization analysis using radiolabeled B20 probe detected two mRNA transcripts of approximately 1.5 and 2.0 kb. Expression data throughout development indicated that these transcripts were present at low levels in nauplii from two of the three crosses examined using broodstocks of Population 1. Higher levels were observed in postlarvae (PL) 6, PL8, and PL10 in one of the three crosses. Individuals from all crosses showed higher levels of expression in the juvenile tail muscle. The mRNA transcript levels were undetected in zoea 3, PL2, and PL4 stages of development and broodstock tail muscle. The levels of expression of B20 mRNA transcripts varied significantly between Populations 1, 2, 3, 4, and wild Ecuadorian individuals as well as between families and within individuals representative of seven families from Population 1. In summary, the B20 clone revealed the presence of two microsatellites that vary in size between populations. These microsatellites will be useful for estimating genetic diversity within and between populations, identifying family-specific markers, and mapping loci responsible for economically important traits in penaeid shrimp. The mRNA levels detected by the B20 clone showed differential expression during development, and the pattern of expression was influenced by the genetic background of the parental crosses used.

French Caucasian population data obtained from fluorescently detected HUMvWFA31/A and HUMF13A01 short tandem repeat loci

Allele and phenotype frequencies for two tetranucleotide STR (short tandem repeat or microsatellite) systems, HUMvWFA31/A and HUMF13A01, were obtained from a sample of approximately 240 unrelated individuals randomly selected from the French Caucasian population. PCR (polymerase chain reaction) products were analysed on 6% polyacrylamide denaturing gels and visualized using fluorescently labelled primers on the automated 373A ABI DNA sequencer (Applied Biosystems Inc.). French Caucasian allele frequencies were compared to other published Caucasian data. Conditions were optimised for the quadruplex PCR amplification of these two STR loci together with the HUMFESFPS and HUMTH01 loci and the quadruplex PCR was also performed on various forensic DNA samples.

Rapid identification of patient specimens with microsatellite DNA markers

Despite the use of standardized clerical and processing procedures in surgical pathology, questions might arise regarding the proper identification of specimens with respect to patient source. Genotypic analysis of microsatellite DNA polymorphisms was used to identify the patient source of two surgical pathology specimens showing carcinoma. Four highly polymorphic microsatellite loci were evaluated in DNA extracted from various formalin-fixed, paraffin-embedded tissues. Using this technique, we determined that the diagnosis of poorly differentiated adenocarcinoma arising from a background of colitis had been assigned to the correct patient, despite the fact that multiple repeat endoscopic examinations, with biopsy specimens, were negative. In the second case, a suspected processing error involving the exchange of specimen accession numbers was resolved when a lymph node containing a microscopic focus of metastatic carcinoma was assigned to the appropriate patient. A multitude (approximately 50,000 to 100,000) of microsatellite loci are distributed throughout the human genome, and many are highly polymorphic. Hence, genotypic analysis using microsatellite loci has a significantly higher power of discrimination than other commonly used methods. The technique is rapid and is particularly well suited to the analysis of small, fixed-tissue specimens.

Microsatellite instability and loss of heterozygosity on chromosome 10 in rat mammary tumors induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine

Microsatellite instability (MI) and loss of heterozygosity (LOH) were examined in mammary tumors induced in Sprague-Dawley x F344 F1 female rats by 2-amino-l-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). Examination of 62 microsatellite loci revealed MI in nine of 15 (60%) PhIP-induced mammary tumors, and five of these MI-positive tumors had mutations in more than one microsatellite locus. In contrast, two of 12 (17%) 7,12-dimethylbenz[a]anthracene (DMBA)-induced mammary tumors were MI positive but had mutations at only one locus each. Further, by using 37 polymorphic markers specific LOH was observed in four of 15 PhIP induced mammary tumors on distal parts of rat chromosome 10, which is homologous to human chromosome 17q with no background level of LOH. Similarly, DMBA-induced mammary tumors showed specific LOH on the same region of chromosome 10. These data suggest that mismatch-repair deficiency and loss of chromosome 10 are involved in carcinogenesis of PhIP-induced rat mammary tumors.

Evaluation of seven microsatellite loci in Simmental cattle

Seven microsatellite loci were evaluated for their suitability for parentage control. The polymerase chain reaction (PCR) was used to amplify the short tandem repeat (STR) loci in separate reactions. The microsatellite polymorphisms were visualized by radioisotopic autoradiographic detection. The microsatellite loci showed extensive polymorphism with allele numbers ranging from 4-23 and polymorphism information content (PIC) values in the range of 0.57-0.87. The analysis of these loci also revealed that they have a 99.9% combined probability of exclusion (PE) of erroneous parentage. The results of this study revealed that a very high probability of exclusion could be reached with only four microsatellite loci.

Long, polymorphic microsatellites in simple organisms

We have examined the phylogenetic distribution of the longest, perfect microsatellites in GenBank. Despite the large contributions of model higher-eukaryotic organisms to GenBank, the selective cloning of long microsatellites from these organisms as genetic markers, and the relative lack of concentration on the microsatellites in lower eukaryotes and prokaryotes, we found that simple organisms, defined here as slime molds, fungi, protists, prokaryotes, viruses, organelles and plasmids, contributed 78 of the 375 examined sequences. These 78 simple-organism microsatellites are characterized predominantly by trinucleotide repeats, nearly half of which lie in exons, and in general show a bias towards A+T rich motifs. Simple-organism microsatellites represented more than once in GenBank displayed length polymorphisms when independent clones were compared. These facts collectively raise speculation as to the role of these 'junk' sequences in such highly economical genomes, especially when precise changes in long microsatellites are known to regulate critical virulence factors in several prokaryotes. Regardless of their biological significance, simple-organism microsatellites may provide a general source of molecular markers to track disease outbreaks and the evolution of microorganisms in unprecedented detail.

Multiple mutations in human cancers

Increasing evidence indicates that most human cancers contain multiple mutations. The exact number of mutations, their origin, and types remain to be determined. An over-riding question is whether the multiple mutations that accumulate in cancers is rate-limiting for the carcinogenic process. In this review we consider the argument that the large numbers of mutations routinely reported in human cancers cannot be accounted for by the rate of spontaneous mutation observed in normal human cells. We will analyze different mechanisms that might account for the accumulation of mutations in cancer cells. We conclude that cancer cells are genetically unstable; i.e., they exhibit a mutator phenotype. The recent reports of microsatellite instability in a variety of human cancers have provided the first strong evidence for the presence of a mutator phenotype in human cancers. However, we still lack information about the relationship between microsatellite instability and mutations that allow cancer cells to proliferate, invade, and metastasize.

The influence of a (GT)29 microsatellite sequence on homologous recombination in the hamster adenine phosphoribosyltransferase gene

Several DNA sequence elements are thought to stimulate homologous recombination, illegitimate recombination, or both in mammalian cells. Some are implicated by their recurrence around rearrangement breakpoints, others by their effects on recombination of extrachromosomal plasmids. None of these sequences, however, has been tested on the chromosome in a defined context. In this paper we show how the adenine phosphoribosyltransferase locus in CHO cells can be used to study the recombinogenic potential of defined DNA sequences. As an example we have measured the effect on homologous recombination of a dinucleotide repeat, (GT)29, which has been shown to stimulate homologous recombination in extrachromosomal vectors 3-20 fold. On the chromosome at the adenine phosphoribosyltransferase locus, however, this sequence shows no capacity to stimulate recombination or to influence the distribution of recombination events.

Microsatellite instability in gastric cancer prone families

We examined for germ-line p53 mutations and microsatellite instability in three gastric cancer patients who had family histories of gastric cancer aggregation. Although no germ-line p53 mutation was detected in these three cases, the replication error (RER) phenotype was observed in two of them. One base deletion in the sequence of ten repeating adenines of the type II transforming growth factor-beta receptor gene was detected in one of these two cases. Furthermore, there were young patients of 50 years and downward in their families. Therefore, it is possible that inherited disorders in mismatch repair systems contribute to high susceptibility to gastric cancers in these families.

Infrequent microsatellite instability during the evolution of myelodysplastic syndrome to acute myelocytic leukemia

Microsatellites are highly polymorphic, short-tandem repeat sequences dispersed throughout the genome. Instability of these repeat sequences at multiple gentic loci may result from mismatch repair errors and occur in hereditary nonpolyposis colorectal cancer and several other sporadic cancers, including chronic myelocytic leukemia as it progresses to blastic crisis. We investigated whether genetic instability occurred as myelodysplasia progressed to acute myelocytic leukemia. To this end, we studied microsatellite instability in 20 patients with myelodysplastic syndrome (MDS). These included five patients with refractory anemia (RA), three with refractory anemia with ringed sideroblast (RARS), nine with refractory anemia with excess blasts (RAEB) and three with chronic myelomonocytic leukemia (CMML). All of these patients transformed to acute myelocytic leukemia (AML) of various subtypes: three patients with M1, 11 with M2 and six patients with M4 (according to FAB classification). The DNA from both the MDS and AML phases of their disease was analyzed at 16 loci, and only four microsatellite instabilities were found in the 240 paired samples (1.6%) analyzed. These results indicate that mismatch repair errors such as microsatellite instability are not important in the evolution of MDS to AML.

Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley

In combination with oligonucleotides of arbitrary sequence, 5' anchored oligonucleotides based on simple sequence repeats were used in polymerase chain reaction amplifications to produce barley DNA fingerprints. The aim of this work was (i) to develop a simple nonradioactive experimental procedure to reveal polymorphism in regions containing SSRs, (ii) to determine the genetic nature of polymorphisms, and (iii) to investigate the efficacy of polymorphisms contained in such fingerprints in disclosing genetic relationships between 14 European barley cultivars with known pedigrees. Different 10-mer oligonucleotides containing a dinucleotide motif were used as single primers and also in pairs with 10-mer oligonucleotides of arbitrary sequence. Further, the arbitrary oligonucleotides were used as single primers to produce RAPDs. Thirteen combinations of primers containing either GT(CA)4 or GC(CA)4 were selected on the basis of number and intensity of scorable bands in silver-stained 7% polyacrylamide gels. Of the fragments scored, 58.4% were polymorphic. Inheritance of these random amplified microsatellite polymorphic fragments (RAMP) was studied in doubled-haploid lines from the F1 of 'Steptoe' x 'Morex'. Fifty percent of the primers generated codominant markers. Genetic similarities between cultivars were estimated from RAMP and RAPD data. Principal coordinate analysis performed on RAMP data revealed a clear separation of winter six-rowed, winter two-rowed, and spring two-rowed barley. The dendograms generated faithfully reflected the genealogies of the barley cultivars. RAPD failed to show clearly the germplasm sources of the experimental cultivars.

Recent evolution of mouse t haplotypes at polymorphic microsatellites associated with the t complex responder (Tcr) locus

Microsatellites closely associated with each member of the Tcp10 gene family were amplified simultaneously from t haplotype and wild-type forms of mouse chromosome 17, by PCR. The t complex responder (Tcr) locus, which plays a central role in transmission ratio distortion, maps within the Tcp10 cluster on the t haplotype. Thus the amplified set of microsatellite loci (referred to collectively as Tcp10ms) provides a direct marker for this central component of the meiotic drive system associated with all naturally occurring t haplotypes. A unique Tcp10ms pattern of microsatellite alleles was obtained for a number of independent, laboratory-maintained complete and partial t haplotypes. Independent t chromosomes found in wild mice from US populations also had unique patterns, even when they were classified within the same lethal complementation group. Wild and laboratory chromosomes in the tw5 group showed similarly-sized but non-identical Tcp10ms patterns, suggesting they share a recent common ancestor. These chromosomes are likely to have derived from an ancestral chromosome within the founding population of North American house mice. The Tcp10ms pattern was also shown to be useful in field studies for distinguishing among independent t haplotypes, when more than one is present within a single population.

Frequencies and sequence characteristics of di-, tri-, and tetra-nucleotide microsatellites in wheat

Microsatellites have emerged as an important source of genetic markers for eukaryotic genomes. In this report, two wheat (Triticum aestivum L.) genomic libraries were screened for several di-, tri-, and tetranucleotide tandem repeats. Clones containing (AC)n, (AG)n, (TCT)n, and (TTG)n repeats were isolated and sequenced. On average, there was one (AC)n microsatellite every 292 kbp and one (AG)n microsatellite every 212 kbp. The trinucleotide tandem repeats (TCT)n and (TTG)n were about 10 times less common than the two dinucleotide tandem repeats tested and tetranucleotide tandem repeats were rare. Many of the microsatellites had more than 10 repeats. The maximum repeat number found for (AC)n was 36 and for (TCT)n was more than 50. The prevailing category of (AG)n microsatellites from (AG)n isolates was perfect repeats. About half of the (AC)n microsatellites were compound repeats, while most of the (TCT)n microsatellites were imperfect repeats. In a small sample, (TTG)n microsatellites consisted mainly of compound repeats. The most frequently associated repeats were (AC)n with (AG)n, (TCT)n with (TCC)n, and (TTG)n with (TGG)n. Among 32 pairs of microsatellite primers surveyed, seven produced polymorphic products in the expected size range and these loci were mapped using a hexaploid wheat mapping population or aneuploid stocks.

[Genetic diagnosis of inborn error of metabolism by microsatellite marker analysis]

We discussed here the usefulness of the microsatellite marker analysis in the prenatal diagnosis of inborn errors of metabolism. Since most inborn errors of metabolism are not common disorders, it is hard to find a common mutation highly useful for the DNA diagnosis. It would be, therefore, more advantageous to diagnose a fetus at risk by analyzing the affected family with multiple highly-polymorphic markers such as the CA repeats. To establish the diagnosis system by the polymorphic markers, it would be a great help to use a human linkage map which contains an increasing number of CA repeat markers.

Ubiquitous somatic alterations at microsatellite alleles occur infrequently in Barrett's-associated esophageal adenocarcinoma

Microsatellite alterations have been documented in a subset of sporadic tumors, including those of the colon, lung, bladder, stomach, and esophagus. This study documented the frequency of microsatellite alterations at 139 loci, comprising predominantly dinucleotide and tetranucleotide repeat units, in 17 cases of primary esophageal adenocarcinoma arising against a background of Barrett's metaplasia. Each tumor demonstrated alterations in at least one locus studied. Widespread microsatellite alterations, occurring at 45.3% (58 of 128) of loci tested, were detected in a single case. The remaining 16 tumors exhibited low levels of microsatellite instability, ranging from 0.8% (1 of 128) to 8.1% (10 of 123) of loci tested. The single case with ubiquitous somatic alterations showed no significant difference in the incidence of novel alleles at di- and tetranucleotide repeat loci. The 16 cases showing a low level of microsatellite alterations demonstrated a 3.3-fold higher incidence of novel alleles at tetranucleotide repeat loci compared to dinucleotide repeat loci. These data suggest that ubiquitous somatic alterations at microsatellite loci, considered a phenotypic expression of defective mismatch repair, occur infrequently in Barrett's-associated adenocarcinoma. However, the majority of these tumors demonstrate a low level of microsatellite alterations, perhaps reflecting the inherent instability of these markers.

Patterns of mutation in cancer cells

The discovery of powerful mutator phenotypes in a subset of colon cancers provides direct support for the hypothesis that destabilization of replication fidelity and repair drive the accumulation of mutations in tumour suppressor or proto-oncogenes. Nevertheless, many important questions remain. The tumour cell lines in which these mutator genes were characterized have many other mutations that may contribute to the mutator phenotype and the characteristic pattern of mutations found in these cells. Thus, mismatch repair deficiency may be necessary for the mutator phenotype, but is it sufficient? Certainly, changes in DNA replication fidelity or cell cycle checkpoint controls may contribute to the mutator phenotype. This question also has important implications for the effect of mismatch repair deficiency on tumour development. Does the mutator phenotype in HNPCC patients arise as a very early event resulting from the loss of the wild type allele or does it arise in later stages only after alterations of cell cycle controls or replication fidelity? Given that eukaryotic cells have numerous homologues of the mismatch repair genes, what are the roles of all these genes? Are these involved in the repair of very specific types of replication errors or do they have other roles in cells? Finally, what mechanisms underlie the accumulation of mutations in other types of tumours? Given the rapid progress made since the isolation of the human homologues of the E coli mismatch repair genes less than 3 years ago, we can look forward to the answers to many of these questions in the near future.

Accurate mapping of the "acid meat" RN gene on genetic and physical maps of pig chromosome 15

It has been shown that a major gene, called RN, is responsible for the RTN technological yield, a meat quality porcine trait. Experimental families informative for the segregation of RN gene were constituted from animals belonging to the Laconie composite line. We have previously mapped the RN gene to Chromosome (Chr) 15 (Milan et al. Genet. Sel. Evol. 27, 195-199, 1995). A Chr 15 map was established with 16 markers. The RN gene was found to be located between markers Sw120 and Sw936, at 2 cM from Sw936 (LOD = 38.1). In addition, by localizing Sw936 at 15q21-22 using DISC-PCR, we also located RN on the physical map.

[The role of retroelements in evolution: an analysis of the suffix element from the Drosophila genome]

The investigation of sequences homologous to the suffix chains from Drosophila genome revealed the central domain of the element homologous to 16S ribosomal sequence from endosymbiotic organisms. The opposite strand of the element encodes C-domains of reverse transcriptase enzyme in F- and Doc-elements. 19 DNA clones possessing PCR-amplified stretches of genomic DNA were sequenced. It was found that micro-satellite sequences (CAACA)n/(TGTTG)n and (TTTGT)n/(CACAAA)n are the target sites for the insertions of suffix copies in heterochromatic regions of Drosophila genome in both orientations. It was found that the presence of decanucleotide GCGGCCCGGG (GC-box) followed by the alternating stretch (A)5(T)4(A)3(T)2(A)1(T)n (AT-box) led to the fixed polarity of the suffix insertions in the same micro-satellite sequences.

Multiple primary cancers with microsatellite instability: report of a case

We report here a patient who developed a variety of tumors both synchronously and metachronously over a 2-year period. The involved organs were the uterus, ureter, and small and large intestines. The patient underwent open surgery 3 times and polypectomies 6 times. Postoperative histopathologic analysis showed 2 adenomas and 8 carcinomas. Genetic analysis revealed microsatellite instabilities at the tested loci in all 10 tumors, indicating that replication errors played an essential role in the tumorigenesis. Early identification of microsatellite instability could be useful for predicting development of additional primary cancers.

Association of celiac disease with microsatellite polymorphisms close to the tumor necrosis factor genes

Celiac disease is tightly linked to the MHC class II region on chromosome 6. We have studied two highly polymorphic microsatellite loci, TNFa and b, near the TNF genes in the class III region of the MHC, for evidence of their association to CD, as compared to a control population. Our findings show that the microsatellite allele most significantly associated with the disease is TNFb3, which is found in 86.3% of CD patients versus 24.5% of controls, with allele frequencies of 0.5392 and 0.1290, respectively (p < 0.001). The TNFa2 allele had a frequency of 0.6122 in CD patients and 0.2627 in controls (p < 0.001), with phenotype frequencies of 87.8% and 50.0%, respectively. TNFa6 and -a11 and TNFb5 have significantly reduced frequencies in CD patients. TNFb3 shows a maximal level of linkage disequilibrium with HLA-DQB1*0201 in celiac patients. However, while the DQB1*0201/TNFa2 haplotype was strongly associated with CD, DQB1*0201 was not significantly in linkage disequilibrium with TNFa2, suggesting that TNFa2 is independently associated with CD. This association could have functional significance as TNFa2 has been correlated with high TNF production.

A homologous and self-replicating system for efficient transformation of Fusarium oxysporum

A highly efficient transformation system has been developed for Fusarium oxysporum f. sp. lycopersici based on the complementation of a nitrate-reductase mutant with the homologous nit1 gene and on the presence of ARS and telomeric sequences in the vector. Preliminary transformation experiments with the niaD gene from Aspergillus niger generated self-replicating plasmids within the transformed entity that contained extra-fungal DNA. A fragment of the extra DNA was inserted into pUC19 together with the F. oxysporum nit1 gene, resulting in plasmid pFNit-Lam. This allowed the isolation of a new linear plasmid within self-replicative F. oxysporum transformants (pFNit-Lam-TLam, linear). The circular form of this vector yielded 5600 fungal transformants per microgram of DNA. All of the transformants contained autonomous linear plasmids harboring direct repeats of fungal DNA at both ends. The sequence of the 1.2-kb fragment from F. oxysporum responsible for autonomous replication, and maintenance as linear plasmid molecules, has been determined. Comparison analysis with the ARS from different organisms has shown that this fragment contained the commonly identified ARS consensus sequence, 5'A/TTTTATA/GTTTA/T3' and, in addition to this core, ten copies of the ARS-box, 5'TNTA/GAA3'. Adjacent to this presumed ARS, the telomeric hexanucleotide sequence (TTAGGG)n was present in six tandem copies followed by 18 copies of its complementary sequence.

The application of FISH techniques for physical mapping in the dog (Canis familiaris)

The abundance of CA/GT repeats in the DNA of the dog (Canis familiaris) has established the importance of polymorphic microsatellites in the development of a low density map of the canine genome. The assignment of linkage groups of markers to chromosomes by physical mapping requires reliable cytogenetic techniques for routine production of metaphase cells. The dog has 78 chromosomes, many of which are smaller and more contracted than those of other mammals. Although the molecular study of inherited disease in dogs has important implications for both improved welfare in dogs and the provision of animal models for human diseases, the small size and large number of chromosomes in the canine genome has discouraged the inclusion of cytogenetic analysis in the planning of relevant research protocols. In this report, Fluorescence In Situ Hybridization (FISH) techniques have been optimized for the physical mapping of probes in C. familiaris. A method to obtain a good yield of early and midmetaphases from short-term peripheral blood cultures and the optimal conditions for hybridization and detection of probes is described. Thirteen microsatellite-containing cosmid probes from a canine genomic library in pWE15, a highly repetitive probe (human ribosomal DNA pHr14E3), and a human X Chromosome (Chr) paint have been mapped. Six microsatellites, two ribosomal sites, and the human paint have been assigned to specific chromosomes.

Induction of frameshift mutations in cultured mammalian cells within a transfected sequence containing a poly(dC-dA).poly(dT-dG) microsatellite

A cultured mouse cell line with an integrated copy of a plasmid that contains a short dinucleotide repeat sequence (microsatellite) has been used to determine the frequencies and types of mutation induced by two frameshift mutagens. The presence of the microsatellite, which consists of 17 repeats of a poly(dC-dA).poly(dT-dG) sequence, disrupts the reading frame of a gene coding for neomycin resistance. Revertants were selected in G418, and mutations were analyzed by PCR. ICR-170 was found to increase the reversion frequency by ten- to 15-fold at its LD50, although most of the frameshifts that it induced were single-base insertions outside the microsatellite sequence. NA-AAF brought about a more modest increase in mutation frequency, but nearly all of the revertants in the NA-AAF-treated cultures had insertions or deletions of multiples of two base pairs within the DNA segment that included the microsatellite. This system can be modified to include different short tandem repeat sequences as targets for testing of compounds that are suspected of having frameshift-inducing activities.

A major locus (RN) affecting muscle glycogen content is located on pig chromosome 15

The RN locus in pigs has a major effect on the amount of stored glycogen in white muscle and affects meat quality. The fully dominant RN- allele, associated with high glycogen content, occurs in the Hampshire breed. We have mapped the RN locus using a large half-sib family comprising one heterozygous RN-/rn+ Hampshire boar mated to homozygous rn+/rn+ Swedish Landrace x Swedish Yorkshire sows. The segregation at the RN locus was inferred from data on glycolytic potential and residual glycogen in white muscle which both showed clear bimodal distributions. Highly significant evidence for genetic linkage was obtained against microsatellite markers on Chromosome (Chr) 15. Multipoint analysis revealed the order Sw1111-8.0-S0088-10.6-RN-4.8-Sw936,Sw906 (recombination estimates are given as Kosambi cM). Comparative mapping data imply that the human homolog of RN is located on Chr 2q.

Microsatellite instability and alterations in the hMSH2 gene in human ovarian cancer

The role of the replication error-positive (RER+) phenotype in the development of specific subtypes of sporadic ovarian carcinomas was examined by screening for the presence of microsatellite instability (MI) in 47 tumors. The overall frequency of ovarian MI was 17% only. However, MI occurred in 50% of the ovarian endometrioid-type tumors, which was significantly more often than in all the other histological subtypes combined (8%). Five of the 8 RER+ tumors exhibited most marked type I instability, possibly representing a different mechanism than for the remaining type 2 tumors. The cDNA of the mutation suppression gene hMSH2, the gene most often associated with MI, was screened for alterations in 8 MI-positive and 5 MI-negative ovarian tumors. Only 3 changes were found. Complete loss of hMSH2 mRNA expression was detected in I tumor, while another expressed only an abnormal transcript containing a deletion of exon 3. One additional RER+ serous adenocarcinoma contained a rare polymorphism with a non-conservative amino acid change. One of 8 RER+ tumors showed loss of heterozygosity at the hMSH2 loci. Genetic instability, caused in part by alterations in the hMSH2 gene, may play an important role in the sporadic endometrioid subtype of ovarian tumors. Other mutator-phenotype genes may be responsible for the remaining cases of RER+ ovarian tumors.

Genetic alterations distinguish different types of ovarian tumors

Seventy-four sporadic ovarian tumors were studied for loss of heterozygosity (LOH) and microsatellite instability (MI) with 20 polymorphic markers on chromosome 17 and at least I marker on every other chromosome. Additionally, activation of the K-ras oncogene was examined through mutation analysis of codon 12. A majority of the tumors analyzed were low grade and/or of the mucinous histologic type. A negative correlation between LOH on chromosome 17 and K-ras activation was observed, with the former alteration present in the majority of high grade serous and endometrioid tumors and the latter most commonly found in the mucinous and low malignant potential (LMP) tumors. In 60% of cases where LOH on chromosome 17 was present, it was observed at all informative markers, indicating chromosome loss. In these cases, frequent events of LOH were observed on the other chromosomes. When confined events of LOH were observed on chromosome 17, fewer events of LOH were observed on the other chromosomes. In the absence of LOH on chromosome 17, LOH on other chromosomes was rare. K-ras activation was most commonly observed in tumors with no LOH events. Two endometrioid tumors and 2 mucinous tumors demonstrated MI. Our data support the involvement of different molecular pathways in the development of different types of ovarian tumors.

Frequency and prognostic evaluation of 3p21-22 allelic losses in non-small-cell lung cancer

Previous loss of heterozygosity (LOH) studies of chromosome 3p loci have displayed a 60% deletion frequency in non-small-cell lung cancers (NSCLC), as opposed to small-cell lung cancers, in which the 3p deletion is consistently found. However, the high stromal-cell admixture found in NSCLC and the use of the Southern-blot method lead to under-evaluation of this frequency. In this study, we used a very precise microdissection technique followed by PCR amplification of 6 3p21-22 polymorphic genomic sequences to analyze LOH in 86 NSCLC and in normal adjacent tissue. We found the sensitivity of the microdissection-PCR-based LOH technique higher than the sensitivity of the Southern-blot technique: 87% of the squamous-cell carcinomas and 84% of the large-cell undifferentiated carcinomas showed a clear LOH for a 3p21-22 locus. All doubly informative cases but 4 showed concordant deletion at all 3p21-22 loci. The analysis of 3p microsatellite sequences displayed only 2 cases of genomic instability, one of them also displaying features of tumoral heterogeneity as regards the instability genotype. Four carcinomas in situ adjacent to these NSCLC showed the same allelic profile as the invasive tumors. The only prognostic factors in this study were the disease stage and histology. The 3p21-22 deletion was not related to the stage of the disease and did not appear to be a significant prognostic factor of survival. 3p21 loss appears, so far, to be the most frequent and the earliest genetic alteration described in NSCLC, but does not seem to carry significant prognostic information in invasive tumors.

Failure to find a chromosome 18 pericentric linkage in families with schizophrenia

A recent report of a possible linkage of bipolar affective disorder to a pericentric region of chromosome 18 initiated the present investigation to search for a similar linkage in 32 families with schizophrenia. The results of a study using 5 markers mapped to this region show negative lod scores and only weak evidence for any linkage by nonparametric analyses. If the previously reported finding is a true positive linkage for bipolar disorder, then either it is unlikely to be related to the genetics of schizophrenia, or the proportion of families linked to this region is small.

A precise meiotic map in the class I region of the human major histocompatibility complex

Human families in which recombinant meiotic event(s) are known to have occurred are powerful tools with which to analyze more precisely the structures of defined genomic regions, especially unstable areas. Such families allow the determination of the haplotypes of each member and, taking into account the recombinant event, it is possible to localize very precisely the point of crossover. Using families in which crossovers between the genes HLA-A and -B have occurred, we have constructed a meiotic map localizing the meiotic breakpoint events with respect to both anonymous markers and the principal genes of the region. Such mapping, which depends on the direct analysis of genomic DNA, is essential for fine structural analysis and is a powerful means of verification of the order and the localization of markers: physical mapping alone, using yeast artificial chromosomes, presents some uncertainties due to the numerous chimeras and inversions that can be produced. The establishment of this map will allow us to determine efficiently the precise location for new markers already localized to the map region. Three microsatellites (D6S265, D6S276, and D6S306), localized in the HLA region by linkage analysis, have been precisely located with respect to the points of recombination in the class I region. The sites of meiotic recombination in the MHC class I region seem to be not randomly distributed but in the majority of cases occurred between HLA-C and the microsatellite D6S265. This study also shows two cases of abnormal segregation of alleles. We discuss how these mutations correspond to a spontaneous mutation event at the somatic or germinal level.

Microsatellites evolve more rapidly in humans than in chimpanzees

Microsatellites are highly polymorphic markers consisting of varying numbers of tandem repeats. At different loci, these repeats can consist of one to five nucleotides. Microsatellites have been used in many fields of genetics, including genetic mapping, linkage disequilibrium analyses, forensic studies, and population genetics. It is important that we understand their mutational processes better so that they can be exploited optimally for studies of human diversity and evolutionary genetics. We have analyzed 24 microsatellite loci in chimpanzees, East Anglians, and Sub-Saharan Africans. The stepwise-weighted genetic distances between the humans and the chimpanzees and between the two human populations were calculated according to the method described by Deka et al. (1994, Genomics 22, 226-230). The ratio of the genetic distances between the chimpanzees and the humans relative to that between the Africans and the East Anglians was more than 10 times smaller than expected. This suggests that microsatellites have evolved more rapidly in humans than in chimpanzees.

Microsatellite instability in human colonic cancer is not a useful clinical indicator of familial colorectal cancer

BACKGROUND & AIMS

Microsatellite instability is a property of most tumors occurring in the context of hereditary nonpolyposis colon cancer. Instability also occurs in 10%-15% of apparently sporadic colorectal cancers, and it has been hypothesized that this instability may indicate a genetic predisposition to colonic cancer. This study evaluated whether there is a clinically useful association between colon cancer instability and a family history of cancer.

METHODS

Colon cancer cases (n = 188) from a population-based study were evaluated for microsatellite instability with 10 polymerase chain reaction primer sets. Instability results were compared with family history and other clinical and biological characteristics.

RESULTS

Microsatellite instability was found in 16.5% of tumors. It was predominantly a feature of right-sided tumors (P = 0.003) and was associated with the youngest and oldest ages at diagnosis (P = 0.01). Instability was not associated with family history of cancer, sex of the individual, or the glutathione-S-transferase mu 1 null genotype.

CONCLUSIONS

Although some very small, and as yet undefined, proportion of colon cancer may be caused by inherited mutations leading to microsatellite instability, tumoral instability by itself is not a marker for familiality and should not be considered as evidence for an inherited syndrome.

Microsatellite sequences in a conifer, Pinus sylvestris

Scots pine (Pinus sylvestris) genomic libraries were constructed and screened with oligonucleotides probes (GT)10, (CT)10, and (AT)10. Eight microsatellites were identified from 6000 clones screened. The longest microsatellite stretch found, (CT)9(N)21(AT)24, was amplified from bud and single pollen grain samples. In order to clarify the complex amplification pattern revealed, two PCR products were sequenced. The size differences were caused both by varying repeat numbers of the microsatellite stretches and by differences in other parts of the amplified sequence. This kind of complex molecular basis of microsatellite amplification within a species has been previously reported. Microsatellite sequences were used as PCR primers to detect polymorphisms and to estimate the abundance of microsatellites.

Infrequent occurrence of microsatellite instability in sporadic and familial breast cancer

Microsatellite instability was analysed in 93 primary breast tumours at 13 chromosomal loci frequently altered in breast cancer. RER (replication errors) were observed at a low (5%) frequency in sporadic, familial and hereditary breast tumours, as well as in breast tumours from patients with multiple primary cancers. Our study suggests that the RER+ phenotype is rare in breast tumours, and that breast cancer is not included in the hereditary non-polyposis colon cancer (HNPCC) syndrome. Moreover, the RER+ tumours revealed an atypical pattern of microsatellite alteration as compared with those usually seen in HNPCC tumours. In agreement with the findings in HNPCC tumours, all RER+ breast tumours were diploid, although having a similar frequency of allelic imbalance as RER- tumours. Thus, mismatch repair deficiency is rare in breast cancer, is most likely caused by somatic mutations, and possibly in a set of DNA repair genes different from that involved in the HNPCC syndrome.

Thyroperoxidase microsatellite polymorphism in thyroid diseases

Autoimmune thyroid diseases (AITD) cluster in families, although the nature of this phenomenon is still poorly understood. One possible approach to the identification of genetic factors contributing to the pathogenesis of AITD is the study of association between polymorphic markers and AITD themselves. In the present study we have analyzed the allelic distribution of sRA-1, a TPO tetranucleotide repeat, among patients with AITD, in comparison with patients with nonautoimmune thyroid diseases and the general population. The polymorphic marker was analyzed by PCR followed by electrophoresis on polyacrylamide denaturant gel. Our data show that no association exists between AITD and any of sRA-1 alleles, despite the important role that TPO plays as a thyroid autoantigen.

Frequency of microsatellite sequences in rice (Oryza sativa L.)

This study was undertaken to estimate the relative frequencies of 13 microsatellite motifs in the rice genome as a basis for efficient development of a microsatellite map. Two dinucleotide, seven trinucleotide, and four tetranucleotide repeat motifs were end labelled and used as hybridization probes to screen genomic and cDNA libraries of rice, cv. IR36. Optimal washing temperatures for identification of clones containing specific microsatellite motifs were estimated based on washing temperatures near Td (dissociation temperature; Td = Tm - 7.6 degrees C). Sequencing of 20 putatively positive clones corresponding to each of 4 microsatellite motifs suggested that while Td provides a useful predictor of washing stringency for most of the repeats studied, those with a very high GC or AT content were most prone to error. The results from screening the rice genomic library suggest that there are an estimated 1360 poly(GA)n and 1230 poly(GT)n microsatellites in the rice genome, and that the relative frequency of different repeats decreased with increasing size of the motif. The most frequently observed microsatellites in the cDNA library were the same as for genomic library, but no poly(CGG)n, poly(ATC)n, or tetranucleotide motifs were observed among cDNA in this study.