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Linkage of biopsy, cancer, and population records aimed at the estimation of family risks in neoplasia: a pilot study
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LINKAGE OF BIOPSY, CANCER, AND POPULATION RECORDS AIMED AT THE ESTIMATION OF FAMILY RISKS IN NEOPLASIA - A PILOT-STUDY
Author(s): BARRAI, I (BARRAI, I); NENCI, I (NENCI, I); GUIDI, E (GUIDI, E); DELLACQUA, G (DELLACQUA, G); FORMICA, G (FORMICA, G); BARBUJANI, G (BARBUJANI, G); MARZOLA, A (MARZOLA, A); MARANI, G (MARANI, G); BARALE, R (BARALE, R); BERETTA, M (BERETTA, M)
Source: JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH Volume: 45 Issue: 2 Pages: 107-111 DOI: 10.1136/jech.45.2.107 Published: JUN 1991
Times Cited: 1 (from Web of Science)
Cited References: 15 [ view related records ] Citation Map
Abstract: Study objective-The aim was to link individual demographic and medical records into sibships to obtain the sibling distribution of biopsies and cancers, and thereby calculate heritability and recurrence risks in families, thus aiding early diagnosis and prevention of cancers.
Design-The 157 823 individual records of the inhabitants of the town of Ferrara in Italy were automatically linked into 106 821 sibships. A 10% sample (10 842 sibships) was then extracted from the distribution of sibships and tabulated, for linkage to medical records.
Patients-The biopsy records at the Institute of Pathological Anatomy of the University of Ferrara were manually linked to cancer records and then to sibships. It was possible to construct the distribution of 2062 biopsies and of 829 cancers in sibships.
Results-From the distribution of biopsies and tumours in sibships, it was possible to estimate the incidence of tumours in the population (0.052) and in siblings of affected (0.083), and to apply to such distributions current methods for the estimate of heritability (h2 = 0.246) and of recurrence risks of tumours in sibships, age independent.
Conclusions-The study shows that the procedure resulting in the estimation of incidences and recurrence risks for tumours could be completely automated, and extended to whole populations and homogeneous subgroups in post industrial cultures
POSSIBLE IDENTITY OF TRANSCRIPTION AND TRANSLATION SIGNALS IN EARLY VITAL SYSTEMS
No full textThe distribution of codons was analysed in three classes of eukaryote proteins having widely different evolutionary rates: 78 histones, 40 tubulins, and seven fibrinogens. In this set of genes, (i) it was confirmed that codons which are components of known transcription signals, like ATA, are used infrequently when a synonym is available, particularly in the more constrained proteins, and (ii) it was observed that the three codons which have an iso-accepting transfer with anticodon UAA, UAG or UGA are also suppressed. Then, the distribution of UAA, UAG and UGA trimers was studied in 498 tDNAs and 198 rDNAs. It was found that these trimers are weakly but significantly suppressed in tDNAs and to a lesser extent in rDNAs. It was advanced that the present suppression of ATA, which codes for Methionine in several mitochondria, and of the TAA, TAG and TGA trimers in tDNAs, might be an indication that at the very early stages of the evolution of translation and transcription the signals for initiation and termination were shared by the two processes
Le paysage monumental de la France autour de l'an mil, sous la direction de Xavier Barrai i Altet, 1987
No full textZadora-Rio Élisabeth. Le paysage monumental de la France autour de l'an mil, sous la direction de Xavier Barrai i Altet, 1987. In: Archéologie médiévale, tome 18, 1988. pp. 404-405
CO-LOCALIZATION OF RARE OLIGONUCLEOTIDES AND REGULATORY ELEMENTS IN MAMMALIAN UPSTREAM GENE REGIONS
No full textIn order to identify putative control signals of gene expression, 634 mammalian DNA sequences spanning 1.8 x 10(6) base-pairs were analysed and the frequencies of 1024 oligonucleotides five bases long (5-tuples) were determined. We defined as rare those 5-tuples having an observed frequency less than 50% of that expected by chance on the basis of base composition, and which had a reduction in frequency not attributable to CpG suppression or to coding constraints. Very few rare 5-tuples were identified; in addition, three oligonucleotides, reverse complements of rare 5-tuples, were found to have a frequency ranging between 0.582 and 0.671. The frequency of most of the rare 5-tuples was higher in 5' promoter regions as compared to exonic segments, so imitating the distribution pattern of known signals. Some of the rare 5-tuples identified by this strategy belonged to a portion of the nine base-pair binding site in promoters, which is also known as the octamer motif. In addition, three of the rare oligonucleotides were found to be located within other regulatory elements, previously identified by techniques of molecular biology. Two rare 5-tuples were found within sites of interaction between DNA and proteins, one of them being a transcriptional factor. The available data about known control sequences involved in gene expression in mammals therefore provide evidence for a role in gene regulation of the rare oligonucleotide selected
Enrichment of oligonucleotide sets with transcription control signals. II: Mammalian DNA.
No full textWe studied the frequency distribution of oligonucleotides 10 bp long in a sample of 1.6 Mb of mammalian genes, containing 579 sequences from GenBank(R) 55.0, with the aim of detecting transcription control signals. 2216 decamers had a frequency higher than 10 times the mean and were subjected to further statistical analysis. For each of the 2216 decamers (parents), we counted the individual frequencies of the 30 decamers differing from the parent by one base mutation (progeny) and then calculated two variance/mean chi squares for the progeny, with and without the parent. We then studied the distribution of the ratio between the two chi squares. Out of 2216 decamers, 346 had a chi square ratio of 1.9 or larger. In this final set, which corresponds to less than 0.033 per cent of all possible decamers, 18 were found to contain 23 eukaryotic transcription control elements 5-10 bp of length, such as Sp1 and others. Furthermore, when compared to 210 random sets containing 346 decamers, this set contains a highly significant excess of the longer signals
Oligonucleotide correlations between infector and host genomes hint at evolutionary relationships
No full textThe frequencies of oligonucleotides of lenght 3-6 were studied in 211 sequences of human DNA (659 kilobases), 22 sequences of DNA of human viruses (120 kbs), in 181 sequences of E. coli (442 kbs), and in 42 sequences of phages of E. coli (137 kbs). The sequences were obtained from Genbank(R) 48. The observed frequencies (O) were compared to the expected frequencies (E) obtained in two ways: 1) according to nucleotide composition for each series, and 2) according to first order Markow chains for triplets, second order for quadruplets, and third order for quintuplets and sextuplets. The ratio O/E was obtained for each oligonucleotide. Then, the correlation between the ratio O/E in a pair of series was calculated. Strong correlations were observed for sequences of man and human viruses, and for E. coli and its phages. Other correlations were small. For higher order Markov chains, there is indication of some correlation also between viruses and phages. It was concluded that through analysis of parallel oligonucleotide series it may be possible to infer some of the complex evolutionary relationships existing between cells and their infectors beyond the level of codon usage
A set of viral DNA decamers enriched in transcription control signals.
No full textWe studied the frequency distribution of oligonucleotides 10 bp long in a sample of 620 Kb of viral genomes, containing 102 sequences from GenBank, with the aim of detecting transcription control signals. Two thousand three hundred decamers had a frequency 10 times higher than the mean and were subjected to further statistical analysis. For each of the 2300 decamers (parents), we counted the individual frequencies of the 30 decamers differing from the parent by one base mutation (progeny) and then calculated two variance/mean chi squares for the progency, with and without the parent. We then studied the distribution of the ratio between the two chi squares. Out of 2300 decamers, 10 times more frequent than average, 479 decamers had a chi square ratio of 1.9 or larger. In this final set, which corresponds to less than 0.05% of all possible decamers, 58 decamers were found to contain viral and eukaryotic transcription control elements, like NF-kB, Sp1 and others. Furthermore, this set contains an excess of signals of length 5, 6, 7, 8, 9 and 10, when compared to 150 random sets, bootstrapped from the same viral genomes
IDENTIFICATION OF A SET OF FREQUENT DECANUCLEOTIDES IN PLANTS AND IN ANIMALS
No full textWe studied the frequency distribution of 1,048,576 oligonucleotides 10 bp long in a sample of 1.961 Mbase of genes from plants, made of 635 sequences extracted from GenBank 71.0, with the aim of detecting transcription control signals. Among all decamers, 3255, or 0.3%, had a frequency 10 times higher than the mean and were subjected to further statistical analysis. For each of the 3255 decamers (parents), we counted the individual frequencies of the 30 decamers (progeny) differing from the parent by one base mutation, and calculated two variance/mean chi-squares for the progeny, with and without the parent decamer. By studying the distribution of the ratio between the two chi-squares we observed that out of 3255 decamers > 10 times frequent than average, 432 had a chi-square ratio > 1.9. In this residual set, which corresponds to < 0.04 per cent of all possible decamers, only 15 known eukaryotic transcription control elements were found; on the other hand, it included 29 decanucleotides that matched with decanucleotides of a set of Drosophila, 24 with a set from mammals, 13 with a set from yeast and four with a set of viruses--all sets identified with the statistical procedures here described. These decanucloetides are highly repetitive and seem to be present throughout all higher organisms, whereas they are uncommon in mammalian viruses
Le paysage monumental de la France autour de l'an mil, sous la direction de Xavier Barrai i Altet, 1987
No full textZadora-Rio Élisabeth. Le paysage monumental de la France autour de l'an mil, sous la direction de Xavier Barrai i Altet, 1987. In: Archéologie médiévale, tome 18, 1988. pp. 404-405
ENRICHMENT OF OLIGONUCLEOTIDE SETS WITH TRANSCRIPTION CONTROL SIGNALS .3. DNA FROM NONMAMMALIAN VERTEBRATES
No full textWe studied the frequency distribution of 1,048,576 oligonucleotides 10 bp long in a sample of 1.072 x 10(6) bases of genes from non-mammalian vertebrates, made of 322 sequences extracted from EMBL(R) 29.0, with the aim of detecting transcription control signals. Among all decamers, 2097 (0.2%) had a frequency 10 times higher than the mean and were subjected to further statistical analysis. For each of the 2097 decamers (parents), we counted the individual frequencies of the 30 decamers differing from the parent by one base mutation (progeny) and we calculated two variance/mean chi squares for the progeny, with and without the parent decamer. By studying the distribution of the ratio between the two chi squares we observed that out of 2097 decamers that occurred > 10 times more frequently than average, 1017 had a chi square ratio of between 1 and 1.5; in this final set, which corresponds to < 0.097% of all possible decamers, 75 decamers were found to contain 100 transcription control elements, like CCAAT and others. The final set contains a high excess of signals when compared to 100 random sets of 1017 decamers. Some of the decamers selected with the procedure are members of consensus sequences rather than unique sequences
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