Characterisation and traceability of extra virgin olive oil and table olive of Azapa variety marketed in Chile using Microsatellite Molecular Markers / Caracterización y trazabilidad de aceite de oliva virgen extra y aceituna de mesa de la variedad Azapa comercializados en Chile mediante marcadores moleculares microsatélites

Chile has two certified origin olive products: Extra-Virgin Olive Oil (EVOO) from Huasco valley and the Azapa variety table olive from the Azapa valley. However, efficient methodologies are needed to determine the varieties and raw materials involved in the end products. In this study, we assessed the size of alleles from ten microsatellites in 20 EVOOs and in leaves and fruits of 16 olive varieties cultivated in Chile to authenticate their origins. The identification of varieties relied on specific allele sizes derived from microsatellites markers UDO99-011 and DCA18-M found in leaves and fruit mesocarp. While most Chilean single-variety EVOOs matched the variety declared on the label, inconsistencies were observed in single-variety EVOOs containing multiple varieties. Our findings confirm that microsatellites serve as a valuable as diagnostic tools for ensuring the quality control of Geographical Indication certification for Azapa olives and EVOO with Designation of Origin from Huasco.

Chile cuenta con dos productos de oliva de origen certificado: El aceite de oliva virgen extra (AOVE) del valle del Huasco y la aceituna de mesa de la variedad Azapa del valle de Azapa. Sin embargo, se necesitan metodologías eficientes para determinar las variedades y materias primas involucradas en los productos finales. En este estudio, evaluamos el tamaño de los alelos de diez microsatélites en 20 AOVEs y en hojas y frutos de 16 variedades de aceituna cultivadas en Chile para autentificar sus orígenes. La identificación de las variedades se basó en los tamaños alélicos específicos derivados de los marcadores microsatélites UDO99-011 y DCA18-M encontrados en las hojas y el mesocarpio de los frutos. Aunque la mayoría de los AOVEs chilenos monovarietales coincidían con la variedad declarada en la etiqueta, se observaron incoherencias en los AOVEs monovarietales que contenían múltiples variedades. Nuestros hallazgos confirman que los microsatélites sirven como valiosas herramientas de diagnóstico para asegurar el control de calidad de la certificación de Indicación Geográfica para aceitunas de Azapa y AOVE con Denominación de Origen de Huasco.

Development of EST-SSR markers in Cenchrus ciliaris and their applicability in studying the genetic diversity and cross-species transferability

Most of the grasses of the genus Cenchrus (20–25 species) and Pennisetum (80–140 species) are distributed throughout the tropical and subtropical regions of the world and reproduce both by sexual and apomictic modes. However, the relationships among the Cenchrus–Pennisetum species are not very clear yet. Molecular markers like expressed sequence tag-simple sequence repeats (EST-SSRs) have been reported to be a better choice for resolving the phylogenetic relationships and to estimate the genetic diversity. The present study describes the identification of EST-SSR markers based on the transcriptome data of Cenchrus ciliaris inflorescence and illustrates the genetic diversity and phylogenetic relationships among these species. Of the 378 primer pairs used across 33 accessions of 21 Cenchrus, Pennisetum, and related grass (Bothriochloa, Dichanthium and Panicum) species, 116 EST-SSR markers were found to be polymorphic with an average polymorphism information content (PIC) of 0.49. Fifty-one EST-SSR loci and 520 alleles showed that where the PIC value is >0.5 there the GAG repeat motif was highly polymorphic. Two EST-SSR markers, CcSSR_80 and CcSSR_102, are polymorphic among the Cenchrus species, while they are absent in Pennisetum and the allied species. Five SSR markers (CcSSR_75, CcSSR_85, CcSSR_87, CcSSR_88 and CcSSR_114) showed 100% cross-transferability among the 21 Cenchrus–Pennisetum species. Species-specific alleles could also be detected for seven species of Cenchrus, Pennisetum and Panicum across 10 SSR markers. Assay of polymorphism across these agamic complexes showed that the three SSR markers (CcSSR_26, CcSSR_97 and CcSSR_109) were associated with Cenchrus–Pennisetum complex, and one (CcSSR_47) with Bothriochloa–Dichanthium complex. Markers with high discriminating power, namely CcSSR_4, CcSSR_38, CcSSR_48, CcSSR_66, CcSSR_67 and CcSSR_70, can be used to estimate the allelic sequence divergence across the sexual and apomictic lineages. Genetic diversity analysis using neighbour-joining (NJ) and principal co-ordinate analysis (PCoA) based approaches showed six and five clusters for the 33 accessions, respectively, having congruence in the pattern of clustering. These accessions were grouped according to their mode of reproduction. Cenchrus and Pennisetum species were grouped separately within the same clade, implying monophyletic group within a ‘bristle clade’. Thus, this study showed high discrimination power of microsatellite (EST-SSR) markers to resolve the phylogenetic relationships.

Genetic Diversity of Plasmodium vivax in Clinical Isolates from Southern Thailand using PvMSP1, PvMSP3 (PvMSP3α, PvMSP3β) Genes and Eight Microsatellite Markers

Plasmodium vivax is usually considered morbidity in endemic areas of Asia, Central and South America, and some part of Africa. In Thailand, previous studies indicated the genetic diversity of P. vivax in malaria-endemic regions such as the western part of Thailand bordering with Myanmar. The objective of the study is to investigate the genetic diversity of P. vivax circulating in Southern Thailand by using 3 antigenic markers and 8 microsatellite markers. Dried blood spots were collected from Chumphon, Phang Nga, Ranong and, Surat Thani provinces of Thailand. By PCR, 3 distinct sizes of PvMSP3α, 2 sizes of PvMSP3β and 2 sizes of PvMSP1 F2 were detected based on the length of PCR products, respectively. PCR/RFLP analyses of these antigen genes revealed high levels of genetic diversity. The genotyping of 8 microsatellite loci showed high genetic diversity as indicated by high alleles per locus and high expected heterozygosity (H(E)). The genotyping markers also showed multiple-clones of infection. Mixed genotypes were detected in 4.8% of PvMSP3α, 29.1% in PvMSP3β and 55.3% of microsatellite markers. These results showed that there was high genetic diversity of P. vivax isolated from Southern Thailand, indicating that the genetic diversity of P. vivax in this region was comparable to those observed other areas of Thailand.

Geographic distribution of genetic variation of natural populations in an endangered and rarely herb Notopterygium forbesii var. oviforme / 中草药

Objective: In order to determine the geographic distribution of genetic variation and structure of natural populations in an endangered and rarely medicinal herb Notopterygium forbesii var. oviforme. Methods The primers of polymorphic microsatellite molecular markers of N. forbesii var. oviforme were firstly developed using the next generation reduced-representation sequencing technology. Then, the genetic polymorphisms of the whole geographical distributional population samples of N. forbesii var. oviforme were investigated based on the polymorphic SSRs. Results:A total of 780 SSR-containing DNA sequences were obtained by genome De novo assembly. Ten pairs of polymorphic SSR primers were developed and used to analyze the genetic variability of 105 individuals from six natural populations that covered the entire geographical distributions of N. forbesii var. oviforme. The results showed that the number of observed alleles (No) per locus varied between 1 and 6 (mean = 3.530). The mean observed heterozygosity (Ho) per population ranged from 0.305 to 0.457. These finds suggested that N. forbesii var. oviforme had the moderate to high level of genetic variability. Bayesian clustering analyses demonstrated that the six natural populations of N. forbesii var. oviforme have formed two clear genetic lineages. The gene flow and/or genetic introgression have occurred between these two groups. Conclusion:The next generation reduced-representation sequencing technology largely enriched SSRs database of N. forbesii var. oviforme. The geographic distribution patterns of genetic variations of N. forbesii var. oviforme may be related to the long evolutionary history of species and pollen dispersal of long distance among different natural populations.

Genetic diversity of Aedes albopictus populations in the coastal areas of southern China, using the microsatellite markers / 中华流行病学杂志

Objective@#To analyze the genetic diversity of Aedes albopictus populations in the coastal areas of southern China by using the microsatellite markers to provide a basis for the control of vectors.@*Methods@#Genetic diversity and clustering analysis of Aedes albopictus populations were studied in the 7 microsatellite loci, in Hangzhou, Ningbo and Yiwu of Zhejiang province, Longyan of Fujian province, Guangzhou of Guangdong province, Nanning of Guangxi Zhuang Autonomous Region and Haikou of Hainan province.@*Results@#Numbers of different alleles (5.429-7.571), effective alleles (2.897-3.632), allele richness (5.236-7.170) and expected heterozygosity (0.538- 0.637) were detected from each of the Aedes albopictus population by using 7 microsatellite markers. The inbreeding coefficients appeared as 0.008-0.332, with heterozygote deficiency, in these populations. Fixation index of the whole populations was 0.058, suggesting that the genetic variation among the 7 populations was 5.8%. Data from the Neighbor-Joining clustering analysis showed that populations from Hangzhou and Yiwu belonged to one branch while Longyan and Guangzhou populations constituted another branch. Aedes albopictus populations of Nanning and Haikou showed great genetic variation but formed a single branch. Bayesian analysis on Aedes albopictus populations showed that the possible number of clusters was 3.@*Conclusions@#Based on 7 microsatellite loci, relatively high genetic diversity and medium level of genetic differentiation that increasing with the geographical distances, were found in these Aedes albopictus populations, from the coastal areas in southern China.

Population Genetics of Plasmodium vivax in Four High Malaria Endemic Areas in Thailand

Recent trends of malaria in Thailand illustrate an increasing proportion of Plasmodium vivax, indicating the importance of P. vivax as a major causative agent of malaria. P. vivax malaria is usually considered a benign disease so the knowledge of this parasite has been limited, especially the genetic diversity and genetic structure of isolates from different endemic areas. The aim of this study was to examine the population genetics and structure of P. vivax isolates from 4 provinces with different malaria endemic settings in Thailand using 6 microsatellite markers. Total 234 blood samples from P. vivax mono-infected patients were collected. Strong genetic diversity was observed across all study sites; the expected heterozygosity values ranged from 0.5871 to 0.9033. Genetic variability in this study divided P. vivax population into 3 clusters; first was P. vivax isolates from Mae Hong Son and Kanchanaburi Provinces located on the western part of Thailand; second, Yala isolates from the south; and third, Chanthaburi isolates from the east. P. vivax isolates from patients having parasite clearance time (PCT) longer than 24 hr after the first dose of chloroquine treatment had higher diversity when compared with those having PCT within 24 hr. This study revealed a clear evidence of different population structure of P. vivax from different malaria endemic areas of Thailand. The findings provide beneficial information to malaria control programme as it is a useful tool to track the source of infections and current malaria control efforts.

Breeding of Zmu-1:DHP inbred strain guinea pig and preliminary analysis of molecular genetic structure of the strain / 中国实验动物学报

Objective To breed a guinea pig inbred strain and set up a method for detection of the microsatellite markers of genetic structure in guinea pigs. Method Using inbreeding methods we try to breed the Zmu-1:DHP inbred strain. With 15 pairs of polymorphism microsatellite primers, the genetic homozygosity of Zmu?1:DHP inbred strain,Zmu?1:DHP outbred strain and Zmu?2:DHP inbred strain ( as control) were examined by PCR. Results After breeding for 13 years, 8 sublines of Zmu?1:DHP inbred strain ( >20 generations) were bred. After identification, the gene frequency of the second subline of Zmu?1:DHP inbred strain was 86. 7%,higher than Zmu?1:DHP outbred strain (6. 7%) and Zmu?2:DHP inbred strain (66. 7%). The average number of loci of Zmu?1:DHP inbred strain was 1. 13,lower than that of Zmu?1:DHP outbred strain (2. 47%) and Zmu?2:DHP inbred strain (1. 33%). The genotypic frequency of Zmu?1:DHP in?bred strain was also higher than that of the other strains. The gene types of Zmu?1:DHP inbred strain were included in the genes of Zmu?1:DHP outbred strain, but Zmu?1:DHP inbred strain was short of 2 characteristic genes. The gene homozy?gous rates of 8 sublines of Zmu?1:DHP inbred strain were different with each other,among them, those of the 2nd and 8th sublines were higher than others. Conclusions There are both homozygosity and specificity in the Zum?1:DHP inbred strain and Zum?1:DHP outbred strain. The second Zum?1:DHP subline becomes a new inbred strain guinea pig. It is es?sential that the subline with the characteristic property is screened from these sublines. The guinea pigs of black Zmu?2:DHP inbred strain carrying microsatellite markers not present in the white strains, may carry optimal genes related with hair color properties.

Mutation analysis of a Chinese pedigree of Leber hereditary optic neuropathy with only male patients / 中华实验眼科杂志

Background Leber hereditary optic neuropathy (LHON) is a maternally inherited disorder characterized by a bilateral acute or subacute painless central visual loss in young adults,predominately in males.So far no one theory can completely explain all clinical manifestations of LHON.Objective This study was to investigate whether there is a linkage between X-chromosomal and mitochondrial mutation in the inheritance of a Chinese LHON pedigree with only male patients.Methods This study was approved by Ethic Committee of Affiliated First Hospital of Zhengzhou University and followed by Declaration of Helsinki.A Chinese LHON pedigree was included in Anyang city from January 2008 to August 2016.Periphery blood of 5-10 ml was collected from 4 sufferers,13 maternal members and 10 non-maternal members for DNA extraction and PCR sequencing.The gene scanning and genotyping analysis were performed by ABI-PRISM 3100 genetic analyzer and Genotyper 3.7 software,and linkage analysis was carried out with Linkage software for the calculation of logarithm of odds (LOD).Mitochondrial DNA (mtDNA) sequence,fluorescence-based Genescan for X-chromosomal sequence were analyzed in the propositus and haplotype was evaluated.Results A total of 5 generations and 71 families were included in the pedigree,with 6 male sufferers,30 maternal members and 41 non-maternal members.The visual acuity was ≤0.10,and the central visual field defection,the optic nerve flushing was found in the acute phase,different levels of the optic nerve fibers atrophy were found in the chronic phase;visual evoked potential (VEP) amplitude was low and peak latency were found in the male patients,and no any ocular abnormality was seen in the maternal members,meeting a maternally inherited characteristics,with the penetranee of 20％.The three primnary mutations were not been found in this family bv PCR sequencing,mtDNA sequencing appeared 31 variation of loci in the proband,including a known G3635A mutation,as well as an unknown ND5 A12340G missense mutation and ND4 T11809C synonymous mutation as well as 28 polymorphism of locus,and the proband was mitochondrial haplotype F1.The maternal families were mutation carriers of G3635A and AI2340G loci,while the same mutation was not found in the normal family members and 107 controls.The maximum two point parametric LOD score was 1.46(θ=0.0) for marker DXS1060,1oeated at Xp22.3,and the two-point and multipoint non-parametric linkage analysis were significant (all at P＞0.05).Conclusions The ND5 A12340G and ND1 G3635A mutations coexist in this LHON family,and the ND5 A12340G mutation is a newly reported mutation.There is no evidence for an X-linked modifiers loci in this Chinese LHON family.

Polymorphism of four microsatellites and their polymerisation effect on litter size in Boer goats

Background: Finding molecular markers linked to quantitative trait loci is the first step in marker-assisted selection (MAS). Microsatellites are excellent molecular markers because of their large numbers, even distribution in the genome, and high polymorphism. In this study, the polymerisation effect of four microsatellites (OarAE101, BM1329, BM143, and LSCV043) on litter size was analysed using microsatellite markers and pedigrees. Results: The results indicate that the polymerisation effect of four microsatellite loci significantly affected the litter size. E5E10F2F6G1G5H6H11 and E3E8F5F7G1G5H3H9 had the highest and lowest litter sizes in the F2 generation, respectively. The polymerisation effect value (v) of the E5E10 genotype was 3.18% higher than that of the E2E7 genotype. The v of genotype F2F6 was 14.47% higher than that of the F5F7 genotype. The v of genotype G1G5 was 58.99% higher than that of the G2G7 genotype. The v of the H6H11 genotype was 5.60% to 49.74% higher than those of the H4H10 and H1H7 genotypes. The v of the H3H9 genotype was 17.22% higher than that of the H1H7 genotype. Conclusions: The results of the present study are vital to improving the reproductive performance in goat breeds MAS.

Genetic variability of Senepol cattle in Colombia using molecular markers / Variabilidad genética de bovinos Senepol en Colombia por marcadores moleculares / Variabilidade genética de gado Senepol na Colômbia por marcadores moleculares

The Senepol beef cattle breed was introduced into Colombia through the use of artificial insemination and embryo transfer from a small nucleus of animals. Objective: to estimate the genetic variability of Senepol cattle in Colombia by heterologous microsatellites and to estimate gene and genotypic frequencies of single nucleotide polymorphic markers through calpastatin (CAST1), calpain (CALP316), and leptin (PB) genes. Methods: 412 blood samples from 28 herds were genotyped for population genetic structure with the STR: INRA32, BM2113, ETH10, BM1824, INRA037, ETH225, INRA064, SPS115, TGLA126, and TGLA122 microsatellite markers. Three SNPs of calpastatin, calpain, and leptin genes were used. Results: all microsatellites and SNP markers were polymorphic. The number of alleles ranged from 4 (BM1824) to 11 (INRA37), and the observed heterozygosity varied between 0.21 (INRA64) and 0.89 (BM2113). Combined probability of exclusion for the microsatellites was higher than 99.99%, indicating the usefulness of this set of markers for parentage testing in Senepol. Conclusions: despite being a small and closed population, this nucleus presents high genetic variability and low inbreeding.

El ganado Senepol fue introducido en Colombia mediante el uso de la inseminación artificial y transferencia de embriones de un pequeño núcleo de los animales. Objetivo: estimar la variabilidad genética del ganado Senepol de Colombia por medio de marcadores microsatélites y estimar las frecuencias alélicas y genotípicas de SNPs en los genes que codifican para la calpastatina (CAST1), calpaína (CALP316) y leptina (PB). Métodos: 412 muestras de sangre de animales pertenecientes a 28 fincas fueron analizados para los STRs: INRA32, BM2113, ETH10, BM1824, INRA037, ETH225, INRA064, SPS115, TGLA126 y TGLA122 y los tres SNPs. Resultados: los microsatélites y los SNPs fueron polimórficos. El número de alelos de los microsatélites variaron entre 4 (BM1824) y 11 (INRA37), la heterocigosidad observada varió entre 0.21 (INRA64) y 0.89 (BM2113). La probabilidad de exclusión para el total de microsatélites fue mayor que 99.99%, indicando que el conjunto de microsatélites pueden ser usados para pruebas de filiación. Conclusiones: a pesar de ser una población pequeña y cerrada, este núcleo presenta una alta variabilidad genética y baja consanguinidad.

O gado Senepol foi introduzido na Colômbia mediante o uso da inseminação artificial e a transferência de embriões de um núcleo pequeno de animais. Objetivo: estimar a variabilidade genética do gado Senepol da Colômbia mediante marcadores microsatélites e estimar as frequências alélicas e genotípicas dos SNPs dos genes de calpastatina (CAST1), calpaina (CALP316) e leptina (PB). Métodos: 412 amostras de sangue de animais pertencentes a 28 rebanhos foram analisadas para os STRs INRA32, BM2113, ETH10, BM1824, INRA037, ETH225, INRA064, SPS115, TGLA126 e TGLA122 e os três SNPs. Resultados: os microsatélites e os SNPs foram polimórficos. O número de alelos dos microsatélites variaram entre 4 (BM1824) e 11 (INRA37), a heterocigosidade observada variou entre 0,21 (INRA64) e 0,89 (BM2113). A probabilidade de exclusão para o total de microsatélites polimórficos foi maior que 99.99%, indicando que o conjunto de microsatélites podem ser usados para testes de filiação. Conclusões: embora seja uma população pequena e fechada, o núcleo apresenta uma alta variabilidade genética e baixa consanguinidade.

Screen and identification of causing-disease gene in a family with a special crystalline autosomal dominant congenital cataract / 中华实验眼科杂志

Background Inheritance is one of main causing-disease factors in congenital cataract.So the screen of causing-disease gene in congenital cataract patients is a critical step.Objective This survey was to investigate the molecular characteristics of a Chinese pedigree with a special crystalline autosomal dominant congenital cataract(ADCC) in Shanxi province.Methods This study was approved by Ethic Commission of Shanxi Eye Hospital.Informed consent was obtained from each subject before any medical examination.Twenty-two families from a pedigree with special crystalline were included in this study.The family members received regular ophthalmologic and general examinations to rule out any concomitant disorders.Blood samples were obtained to extract the DNA from all the subjects.Twenty-two fluorescent labeled microsatellites were selected from 17 causing genes of ADCC and amplified and screened for the linkage analysis.LOD was calculated and the candidate gene was directly sequenced.Results Ten individuals with congenital cataract were found in the family with the similar phenotype.The inheritance mode complied with the autosomal dominant pattern.Linkage analysis indicated a gene chain at D2S325 and D2S2358 with the LOD value 1.20(θ =0) and 0.22(θ =0).A known c.C70A(p.P23T) missence mutation at the coding region of CRYGD gene was detected by direct sequence.Conclusions A missense mutation P23T of the CRYGD gene cause the autosomal dominant congenital nuclear cataract with the special phenotype.

Molecular Biological Differences Between Younger and Older Breast Cancer Patients Based on the Status of a Microsatellite Marker

PURPOSE: Younger women exhibit more aggressive pathological features of breast cancer than older women, based on previous studies. We wished to evaluate any molecular biological differences in breast cancer between younger and older women by determining the status of a microsatellite marker. METHODS: Microsatellite instability (MSI) and loss of heterozygosity (LOH) were investigated in paired tumour and normal tissue DNA from 32 younger (age less than 40 years old) and 32 older (age more than 50 years old) breast cancer patients with 12 simple repeated primer sets. RESULTS: MSI was observed at a single locus in 5 (15.6%) of the younger patients. In older patients, MSI was observed at a single locus in 5 (15.6%) and at multiple loci in 1 (3.1%) of the older patients. LOH was noted at a single locus in 7 (21.8%) and at multiple loci in 22 (68.7%) of 32 younger patients. In older patients, LOH was noted at a single locus in 9 (28.1%) and at multiple loci in 15 (46.9%). The greatest frequency of LOH was at loci UT5320 (37.5%), D8S321 (34.4%), D9S242 (31.3%), and D19S394 (31.3%) in younger patients and at loci L17686 (34.4%) and D19S394 (28.1%) in older patients. LOHs at D19S394 and L17686 were highly identified in both age groups. LOHs at D9S242 and D8S321 were significantly higher in the carcinomas of younger women (P=0.013, P=0.016, respectively). The LOH status was unrelated to clinical stage, nodal status, tumour size, histological grade or estrogen receptor (ER) status. A LOH at D8S321 was associated with tumor size (P=0.048) and a LOH at UT5320 was associated with histological grade (P=0.012) and ER status (P=0.018). CONCLUSION: These results indicate that the pattern of chromosomal alterations are not exactly the same, especially at loci D9S242 and D8S321, in the carcinomas of the two age groups and suggest that the molecular pathogenesis of the carcinomas is not similar.

Putative Tumor Suppressor Gene Loci onChromosome 20q in Intrahepatic Cholangiocellular Carcinoma that were Found by Microsatellite Marker Analysis

PURPOSE: Intrahepatic cholangiocellular carcinoma (ICC) is the second most common malignant tumor in the liver, and it arises from epithelial cells in the intrahepatic bile duct. While the reported risk factors include liver fluke infection, hepatolithiasis and sclerosing cholangitis, the genetic mechanisms involved in the development of ICC are not well understood, and only a few cytogenetic studies of ICC have been published. We recently found genetic imbalance on chromosome 20q in ICC with using Comparative Genomic Hybridization. So, we tried to find gene loci on chromosome 20q. (ED note: what kind of loci were you looking for) METHODS: We used 16 fresh frozen ICC tumor tissues and the paired normal liver tissues for DNA extraction. A set of primers for 10 microsatellite loci on chromosome 20q13-qter, based on an updated GeneMap99 and Ensemble, was purchased from Research Genetics. The markers selected for testing exhibited high levels of heterozygosity and relatively uniform distributions. Loss of heterozygosity (LOH) was analyzed by an automatic DNA analyzer. Using the Ensemble Web site, mining of putative tumor suppressor genes were developed between microsatellite markers that showed LOH. RESULTS: In one case, microsatellite instability (MSI) was found in all the markers except D20S196, and MSI was found in only one marker, d20S196, in another case. (Ed note: check this and it wasn't clear.) The most frequent region which have LOH on chromosome 20q13-qter was on D20S109 and D20S196, and their invidence was 12.5%. (ED note: the last part of the sentence makes no sense at all. You have to rewrite it.) D20S174, D20S107, D20S170, D20S96 and D20S119 were 6.3% and D20S836, D20S886 and D20S were 0%. (ED note: this sentence also makes no sense. They were 6% and 0% of what?) We found eight genes between D20S109 and D20S196: PTPN1, QSNf41 HUMAN, CT175 HUMAN, PARD6B, BCAS4, TMSL6, ADNP and DPM1. Among these, PTPN1, PARD6B and BCAS4 are well known oncogenes, so the other five genes are thought to be putative tumor suppressor genes. CONCLUSION: Using this approach, we identified two distinctive allelic losses defined by microsatellite markers as follows; D20S109 and D20S196. We identified five genes which can make contribution to the development or progression of intrahepatic cholangiocellular carcinoma. Further study will be carried out to confirm these genes have a critical role in the development or progression of intrahepatic cholangiocellular carcinoma using immunohistochemical study or other molecular biology work.

Identification of Tumor Suppressor Loci on the Long Arm of Chromosome 15 in Primary Small Cell Lung Cancer

Small cell lung cancer (SCLC) frequently shows a loss of heterozygosity (LOH) on chromosome 15q. In order to define the commonly affected region on chromosome 15q, we tested 23 primary SCLCs by microsatellite analysis. By analyzing 43 polymorphic microsatellite markers located on chromosome 15q, we found that 14 (60.8%) of 23 tumors exhibited a LOH in at least one of the tested microsatellite markers. Two (14.3%) of the 14 tumors were found to have more than a 50% LOH on chromosome 15q. LOH was observed in five commonly deleted regions on 15q. Of those regions, LOH from D15S1012 to D15S1016 was the most frequent (47.8%). LOH was also observed in more than 20-30% of tumors at four other regions, from D15S1031 to D15S1007, from D15S643 to D15S980, from D15S979 to D15S202, and from D15S652 to D15S642. Four of the 23 tumors exhibited shifted bands in at least one of the tested microsatellite markers. Shifted bands occurred in 3.2% (29 of 914) of the loci tested. Our data suggests the presence of at least five tumor suppressor loci on chromosome 15q in SCLC, and further that these may play an important role in SCLC tumorigenesis.

Development of Microsatellite Markers for Diagnosis of Autosomal Dominant Polycystic Kidney Disease / 대한신장학회잡지

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a common hereditary disorder characterized by the slow growth of fluid-filled cysts that distort the renal architecture and lead to a lethal condition. Genetic heterogeneity in ADPKD has been demonstrated after a linkage was initially discovered for PKD1 on chromosome 16p13.3. The second gene, PKD2, has been localized on chromosome 4q21-23 and accounts for approximately 15% of affected families. PKD2 is a -50kb sized gene and has at least 15 exons. PKD2 gene product, polycystin-2, has 968 amino acids and seems to be a transmembrane protein. To find novel microsatellite markers of PKD2, we isolated a PAC DNA containing PKD2 by screening a PAC genomic DNA library. The isolated PAC, PAC47, was restriction-mapped. In addition, a pUC library was constructed by partially digesting PAC47 with Sau3AI. Based on the results of random sequencing of the pUC library, we found several clones that had repeat sequence. By analyzing the polymorphism of these clones, a novel microsatellite marker was discovered that has 0.5945 in HET score. Furthermore, HET score of microsatellite markers neighboring PKD2 was determined in Korean population and then this HET score was compared with that of genome database(GDB). In diagnosis of ADPKD in Korean, these results will improve the efficiency of linkage analysis.

Allelotyping and Comparative Genomin Hybridization Studies in Papillary Thyroid Carcinomas and Follicular Adenomas / 대한내분비학회지

BACKGROUND: In our previous study, the prevalence of the known causes of thyroid tumorigenesis was relatively rare in Korean population, suggesting genetic and environmental differences exist. Screening of genetic alteration in papillary thyroid carcinoma(PTC) and follicular adenoma(FA) in whole genomic scale was needed prior to search on individual genes of possible causes. METHODS: Ten cases of PTC without ret/PTC-I, -2, -3 rearrangement and 5 cases of follicular adenoma were included in the study of microsatellite marker allelotyping. Sixty two microsatellite markers available, were chosen to cover the known sites of loss of heterozygosity(LOH) involved in thyroid tumors, tumor suppressor genes and terminal portion of each chromosomes. PCR was performed on tumor DNA and leukocytes DNA from each patient with MDE gel electrophoresis to detect LOH. Same specitnens as above, 3 case of normal thyroid tissues and NPA, ARO cell lines were included in the study of comparative genomic hybridization(CGH). Tumor and control DNAs were hybridized to metaphase chromosome with differential stainings with fluorescein and rhoda-mine-dUTP. Obtained results were analyzed by multicolor fluorescence computer assisted image analyzer. RESULTS: In allelotyping, LOH were detected in 5 cases of PTC, 2 cases on D10S1435, 1 case each on D2S1780, DSS1099, D11S1986, D16S539, 1 case of PTC revealed LOH on DSS1099, D11S1986. In FA, LOH were detected in 3 cases on D1S534, D1S226, Dl 1S907, D22S683, DXS9807. In CGH, Xp addition was noticed in 1 case of PTC, 12q and 10p addition was noticed in 1 case each, 16q deletion and 17q addition in 1 case of FA. CONCLUSION: No hot spot of LOH was noticed in microsatellite marker allelotyping, neither of common chromosomal change in CGH study suggesting unbalanced translocation or gene amplification more than 5-10 Mb may be involved in the genetic alteration of PTC and FA.

Identification of Genetic Locus for Disseminated Superficial Actinic Porokeratosis / 中华皮肤科杂志

Objective To identify the genetic locus for disseminated superficial actinic porokeratosis(DSAP).Methods Genome DNA was extracted from the whole blood of the family members of a pedigree of DSAP.Genotyping on chromosome12q that had been identified was performed by using7microsatellite mark-ers to scan the family members of DSAP and analysed with LINKAGE(5.1Version).Results A maximum2-point lod score of5.15with marker D12S79at a recombination fraction(?)=0.00was found.Conclusion Our study supports that DSAP gene localizes at the long arm of chromosome12,which was first reported in the literature.