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Medical Research Institute of Radiology, Russian Academy Forty-eight cases of familial disease (24 families) (4.3%) were identified among 1,118 patients with well-differentiated thyroid carcinoma who had been either examined or treated at the Clinic of Medical Research Institute of Radiology (1995-2004). In 86% of the study group, papillary thyroid carcinoma (PTC) was associated with tumor of the identical histological pattern while the remaining families revealed association with follicular or medullary thyroid cancer. Carcinoma inheritable from mother was the most frequent (75%). No differences in manifestation, histological pattern, stage or clinical course were established following a detailed evaluation of clinico-morphological data on 43 familial and 172 sporadic (control) cases in both groups. The analysis pointed to a significantly higher incidence of concomitant thyroid pathology in the familial thyroid cancer group. Molecular-genetic study of RET-protooncogene and gene BRAF in 6 blood samples from PTC-bearers established RET-mutation (mother and daughter) in codon 891 (exon 15) G2673A (TCG->TCA). No mutation in BRAF was found.

Frequency of RET/PTC rearrangement and somatic BRAF mutation was investigated in patients with papillary thyroid cancer (PTC) vis-a-vis relevant demographic and clinico-pathological features. The study group included 76 patients with a female/male ratio of 4.8:1; mean age - 45.7 +/- 9.7 yrs. BRAF mutation was identified in 49 (65%) (V600E--47, KSRWS600--1 and E585K--1). RET rearrangement was detected in 9 (12%): RET/PTC1--5, RET/PTC3--2, unspecified RET/PTC--1 and delta RET/PTC--1. It was age at diagnosis alone that proved to be consistently associated with BRAF mutations (p = 0.017). Younger tumor patients were mostly prone to RET/PTC rearrangement (p = 0.08). No correlation between mutation and clinico-pathological features was established.

The GIPC1 gene product promotes clustering of some transmembrane receptors, including those involved in carcinogenesis, and protects them against ubiquitin-dependent degradation. The 5' untranslated region of GIPC1 contains a polymorphic trinucleotide CGG repeat, which has not been characterized earlier. In the present study, we have carried out comparative analysis of the allele and genotype frequencies of this repeat in 129 samples of breast cancer (BC), 58 samples of non-small cell lung cancer (NSCLC), and 215 samples of healthy donors. The CGG repeat in the 5' untranslated GIPC1 gene region was shown to be highly polymorphic and represented by at least eight alleles. Alleles CGG10-13 were major, occurring at frequencies of 22, 41, 27, and 9%, respectively; the total frequency of the remaining alleles was approximately 1%. Heterozygosity of the CGG repeat was 0.70. Allele CGG12 was shown to be associated with high risk of developing NSCLC (alpha = 0.05).

Multiplex methylation-sensitive PCR and methylation-specific PCR were employed in studying the methylation of CpG islands in the p16/CDKN2A and p14/ARF promoter and the first exon regions in non-small cell lung cancer (54 samples) and acute B-cell lymphoblastic leukemia (61 samples). Differences in methylation were detected between types of neoplasia as well as between CpG islands studied within the same types of tumors. High level of the p16/CDKN2A first exon CpC island methylation was revealed in non-small cell lung cancer (68%) and in acute B-cell lymphoblastic leukemia (55%) and the CpG island of p14/ARF first exon was nonmethylated in these types of tumors. The methylation of CpG-rich fragments of genes p16/CDKN2A and p14/ARF promoters was analysed. As was found out, CpG islands located in 5' areas of one and the same gene can differ in methylation frequencies. The comparison of sensitivity between methylation-specific PCR and methylation-sensitive PCR used in the methylations studies was carried out.

Rearrangements of the RET proto-oncogene (RET/PTC) and BRAF gene mutations are the major genetic alterations in the etiopathogenesis of papillary thyroid carcinoma (PTC). We have analyzed a series of 118 benign and malignant follicular cell-derived thyroid tumors for RET/PTC rearrangements and BRAF gene mutations. Oncogenic rearrangements of RET proto-oncogene was revealed by semiquantitative RT-PCR of simultaneously generated fragments corresponding to tyrosine kinase (TK) and extracellular RET domains. The clear quantitative shift toward the TK fragment is indicative for the presence of RET rearrangements. The overall frequency of RET/PTC rearrangements in PTC was 14% (12 of 85), including 7 RET/PTC1, 2 RET/PTC3, 1 deltaRFP/RET and 2 apparently uncharacterized rearrangements. The most common T1796A transversion in BRAF gene was detected in 55 of 91 PTC (60%) using mutant-allele-specific PCR. We also identified two additional mutations: the substitution G1753A (E585K) and a case of 12-bp deletion in BRAF exon 15. Moreover, there was no overlap between PTC harboring BRAF and RET/PTC mutations, which altogether were present in 75.8% of cases (69 of 91). Taken together, our observations are consistent with the notion that BRAF mutations appear to be an alternative pathway to oncogenic MAPK activation in PTCs without RET/PTC activation. Neither RET/PTC rearrangements nor BRAF muta-tions were detected in any of 3 follicular thyroid carcinomas, 11 follicular adenomas and 13 nodular goiters. The high prevalence of BRAF mutations and RET/PTC rearrangements in PTCs and the specificity of these alterations to PTC make them potentially important markers for the preoperative tumor diagnosis.

The review considers the epigenetic defects and their diagnostics in several hereditary disorders and tumors. Aberrant methylation of the promoter or regulatory region of a gene results in its functional inactivation, which is phenotypically similar to structural deletion. Screening tests were developed for Prader-Willi, Angelman, Wiedemann-Beckwith, and Martin-Bell syndromes and mental retardation FRAXE. The tests are based on allele methylation analysis by methylation-specific or methylation-sensitive PCR. Carcinogenesis-associated genes (RB1, CDKN2A, ARF14, HIC1, CDI, etc.) are often methylated in tumors. Tumors differ in methylation frequencies, allowing differential diagnostics. Aberrant methylation of tumor suppressor genes occurs in early carcinogenesis, and its detection may be employed in presymptomatic diagnostics of tumors.

Multiplex methylation-sensitive PCR was employed in studying the methylation of CpG islands in the RB1, p16/CDKN2A, p15/CDKN2B, p14/ARF, CDH1, HIC1, and N33 5' regions in non-small cell lung cancer (51 tumors). Methylation was observed for the two suppressor genes involved in controlling the cell cycle through the Cdk-Rb-E2F signaling pathway, RB1 (10/51, 19%) and p16 (20/51, 39%). The highest methylation frequencies were established for CDH1 (72%) and HIC1 (82%). The CpG islands of p14 and p15 proved to be nonmethylated. At least one gene was methylated in 90% (46/51) tumors and no gene, in 10% (5/51) tumors. In addition, the genes were tested for methylation in peripheral blood lymphocytes of healthy subjects. Methylation frequency significantly differed between tumors and normal cells in the case of RB1, p16, CDH1, HIC1, and N33. Gene methylation frequency was tested for association with histological type of the tumor and stage of tumor progression. Methylation index of a panel of tumor suppressor genes was established for groups of tumors varying in clinical and morphological parameters.

Polymorphic alleles of CYP17 and CYP19, which are involved in estrogen biosynthesis, were tested for association with breast cancer (BC). Microsatellite (TTTA)n and 3-bp deletion of CYP19 and single-nucleotide polymorphism T27C of CYP17 were analyzed in 123 BC patients and 119 healthy women. Of the six (TTTA)n alleles observed, allele (TTTA)8 proved to be associated with BC (11.8% vs. 6.3%, P = 0.04). Genotype A2/A2 of CYP17 was also associated with BC (32.5% vs. 20.2%, P = 0.04). Risk of BC was especially high in the presence of both factors (7.3% vs. 0%, P < 0.01). Allele (TTTA)8 and genotype A2/A2 were assumed to be risk factors of BC.

Multiplex methylation-sensitive PCR was employed in studying the methylation of CpG islands in the RB1, p16/CDKN2A, p15/CDKN2B, p14/ARF, CDH1, MGMT, HIC1, and N33 promoter regions in breast carcinoma (105 tumors). Methylation was often observed for the two major suppressor genes involved in cell-cycle control through the Cdk-Rb-E2F signaling pathway, RB1 (18/105, 17%) and p16 (59/105, 56%); both genes were methylated in 13 tumors. Methylation involved p15 in two (2%) tumors; CDH1, in 83 (79%) tumors; MGMT, in eight (8%) tumors, and N33, in nine (9%) tumors. The p14 promoter was not methylated in the tumors examined.

A PCR-based survey of allelic polymorphism of three microsatellite markers, DXS998, DXS548, and FRAXAC1, mapped to chromosome region Xp27.3, and two microsatellite markers, DXS8091 and DXS1691 located on Xq28 was carried out using a series of DNA samples obtained from 98 unrelated individuals from Russia. The number of alleles detected on electrophregrams for each marker tested was 4, 6, 4, 5, and 3, respectively. The values of heterozygosity index for the markers examined were 0.65, 0.27, 0.38, 0.70, and 0.29, respectively. The observed distribution of the allelic frequencies for each microsatellite marker examined fitted Hardy--Weinberg expectations. The values of individualization potential determined for each marker were 0.24, 0.53, 0.43, 0.12, and 0.52, respectively. In the sample tested the genotype distribution with regard to above loci was determined. The perspectives of using the analyzed allelic polymorphisms for indirect DNA diagnostics of the monogenic diseases located in this chromosome region (X-linked mental retardations, FRAXA and FRAXE) as well as for human population genetics and personal identification is discussed.

Multiplex methylation-sensitive PCR was employed in studying the methylation of the RB1 and CDKN2A/p16 promoter regions in 52 retinoblastomas. Aberrant methylation inactivating RB1 was detected in 14 (27%) tumors. Methylation of p16 was for the first time observed in retinoblastoma (9 tumors, 17%). Both promoters proved to be methylated in two tumors. In four tumors, aberrant methylation was combined with structural defects of both RB1 alleles. Aberrant methylation of the p16 promoter was the second mutation event in two tumors and was not accompanied by RB1 defects in one tumor. Complex testing for RB1 mutations, loss of heterozygosity, and functional inactivation of the two genes revealed a molecular defect in at least one allele in 51 (98%) tumors.

The spectrum and frequencies of RB1 structural defects were studied in tumors and peripheral blood lymphocytes of patients with various forms of retinoblastoma. Single strand conformation polymorphism (SSCP) and heteroduplex (HA) analyses, along with direct sequencing, revealed 47 mutations, including 24 new ones. Of these, 42.5% were nonsense mutations, 15% were missense mutations, 15% affected splicing sites, and 27.5% were frameshifts resulting from microdeletions or microinsertions. Six polymorphisms were found, including three new ones located in the coding region. Microsatellite analysis with markers Rbint2, Rbint20, D13S262, and D13S284 revealed a loss of heterozygosity for at least one marker in 71% tumors.

The first experience with molecular diagnosis of retinoblastoma (RB) in Russia is presented. A protocol based on the use of up-to-date molecular diagnostic methods helps detect structural and functional abnormalities in RB1 gene, diagnose RB in disputable cases and at early stages of the disease. Forty-five families with various forms of RB were examined. Twenty-three mutations in various sites of RB1 gene were characterized. Abnormal methylation in the promotor area of RB1 gene was detected in 20% cases and loss of heterozysity by intragene microsatellite markers was detected in 70% cases. Hence, the causes of RB were detected in 80% families, which led to early diagnosis in close relatives of patients and helped evaluate the repeated risk of the tumor in families of patients with RB.

The paper presents current data on theepigenetic regulation of gene expression in malignant tumors. Methylation of CpG islands in the gene promoter regions not accompanied by DNA structural changes leads to gene inactivation. The analytical methods of DNA methylation are described in detail. Methylation of certain genes in different tumor types are examplified. Since methylation is an early marker of carcinogenesis, there is an opportunity of elaborating of prospective diagnostic protocols.

A number of genetic syndromes and cancer are caused by chromosomal microstructural rearrangements. It is sometimes impossible to detect this pathology microscopically. A complex of molecular methods makes it possible to detect subchromosomal deletions, point mutations, and functional anomalies on the respective genes, which cause a disease. Achievements of comprehensive analysis have been demonstrated in cases of some well-known diseases, the Prader-Willi syndrome, Engelmann's syndrome, the Martin-Bell syndrome, hereditary multiple exostotic chondrodysplasia, and retinoblastoma. DNA-diagnosis protocols are the result of this study.

A molecular-genetic characterization of deletions in part of chromosome 8q24.1 was performed in patients with Langer-Giedion syndrome (six patients) and triho-rhino-phalangeal syndrome type I (three patients) by means of Southern blot hybridization analysis, restriction fragment length polymorphism and single-strand conformation polymorphism, analysis. Four families with multiple exostosis chondrodysplasia (MECD) also underwent the same analysis. Results of deletion mapping allowed determination of the probable region of localization of the proposed gene of MECD at D8S67 locus. By means of a polymorphic DNA probe obtained from the locus an additional hybridization signal was revealed only in patients with MECD. Other polymorphic DNA probes and microsatellite sequences confirmed the results of deletion mapping and detected haplotypes on the chromosomes with a mutation in the proposed MECD gene.

A male infant is described with dysmorphology of the head and face, neck, extremities and genitalia, as well as growth and mental retardation and with the de novo interstitial deletion of the proximal segment of the long arm of chromosome 1-del (1) (q22-q25). Comparison of the phenotypic characteristics of this patient with those of previously described patients with similar deletion confirms the existence of the proximal 1q deletion syndrome.

Two mentally retarded girls with a small metacentric nonsatellite extrachromosome were examined. Probands were found to share many clinical features: asthenic constitution, microcephalia, low-set malformed ears, high arched palate, long fingers and toes, a wide gap between first and second toes, clinodactyly of the 1st and 5th fingers, scoliosis. The extrachromosome was unequivocally interpreted as an isochromosome for the short arm of chromosome 18. Review of 12 i (18p) cases permits characterizing a syndrome of tetrasomy 18p.

Clinical genetic analysis of distal trisomies 1q, based on the study of a t(1; 6) (q42.1; p24) family and the literature data, was performed. It was demonstrated that phenotypical manifestations of the trisomy are formed by nonspecific anomalies, due to imbalance as such, and by rather specific anomalies caused by triplication of a "critical segment". 1q42-1qter appeared to be such a segment for distal trisomy 1q.

Del(8) (q24.11-q24.13) were detected in 3 patients with typical Langer-Giedion syndrome (LGS) and studied by high-resolution methods. Analysis of the literature strongly suggests the chromosomal ethiology of the LGS, because in all patients examined in detail a deletion of the segment 8(q24.11-q24.13) was revealed, which is critical for the LGS. Interrelationships between the LGS and two monogenic conditions-tricho-rhino-phalangeal syndrome type I and multiple exostoses are discussed. The possible role of c-myc oncogene in exostoses' (including those in LGS) origin is anticipated.

Three syndromes of multiple endocrine neoplasia (MEN) have been identified to date: MEN--I, IIa and IIb. They involve various combinations of endocrine neoplasia and occur mostly in young patients. Predisposition transmission mechanism is autosomal-dominant with total penetration and variable expressiveness. Patients' families should undergo screening which involves identification of biochemical markers and cytogenetic examination. This would allow identification of subjects at high risk for cancer and improvement of early diagnosis.

The family, where 2 children had partial trisomy 2q33-q ter, due to paternal translocation t(2;18) (q33;p11.1), was examined. The analysis of 36 cases of trisomy 2q showed that the forms connected with parental chromosomal rearrangement prevailed in the genesis of trisomy 2q. Moreover, the balanced carrier-mothers were more common than fathers. The 2q34-q ter segment may be considered "critical" for occurrence of trisomy 2q syndrome. In case of equal triplication, the similarity between the patients within the same family is greater than between those from different families. The value of intragroup similarity between the patients with equal trisomies may be used for evaluation of phenotypical similarity at different triplicated segments.