Markers For Identification Of Individuals Research Articles

Conventional Gel Electrophoresis-Resolvable Insertion/Deletion Markers for Individual Identification and Analysis of Population Genetics in Red-Crowned Cranes in Eastern Hokkaido, Japan.

Simple SummaryThe red-crowned crane is an endangered bird species in the Far East Eurasian continent and Hokkaido, Japan. Individual identification has been achieved with banding and installed transmitters in only a few cranes, though individual identification is essential for various assessments of cranes on their behavioral characteristics, for example. An insertion/deletion (InDel) mutation is a mutation ranging from 1 to 50 bp and is very useful for genetic studies. If primer sets across InDels (>20 bp) can be designed, an InDel polymorphism can be determined with conventional agarose gel electrophoresis, as reported in some plant species. We found a sufficient number of InDel primer sets to be used for individual identification and analysis of population genetics of red-crowned cranes in Hokkaido. The method has additional advantages, such as convenience and low cost, without sequencing and an expensive apparatus.Red-crowned crane Grus japonensis is an endangered species in two separate populations: the mainland population in the Eurasian continent and the island population in eastern Hokkaido, Japan. We found 11 insertion/deletion (InDel) markers in the genome of the red-crowned crane and designed primer sets across these InDels that can be analyzed with conventional agarose gel electrophoresis. Sixty-six samples of whole blood and skeletal muscle obtained from red-crowned cranes, including 12 families in eastern Hokkaido from 1994 to 2021, showed different patterns in gel images of 11 InDel PCR reactions except for two pairs. The combined non-exclusion probability of the 11 markers indicates that individuals can be determined with a probability of 99.9%. In 39 non-relative chicks, the expected heterozygosity (He) was 0.316, suggesting low genetic diversity. This might not be caused by high levels of inbreeding since the average FIS was not significantly different from zero (0.095, p = 0.075). The results suggest that the 11 InDel primer sets can be used for fairly accurate individual identification as well as genetic population analyses in red-crowned cranes in the island population.

Development of a New Microsatellite Markers for Individual Identification and Paternity Evaluation in Hanwoo

Development of a New Microsatellite Markers for Individual Identification and Paternity Evaluation in Hanwoo

Genetic individualization of sable (Martes zibellina L. 1758) using microsatellites

ABSTRACTGenetic individualization based on non-invasive sampling is crucial for estimating the numbers of individuals in endangered mammalian populations. In sable (Martes zibellina)-poaching cases, identifying the number of animals involved is critical for determining the penalty. In addition, investigating animal numbers for wild sable populations requires genetic individualization when collecting several samples in neighboring regions. Microsatellites have been demonstrated to be reliable markers for individual identification. Thirty-three microsatellite loci derived from Mustelidae were selected to develop a genetic individualization method for sable. Three reference populations containing 54 unrelated sables were used to calculate allele number, allelic frequencies, and the polymorphic information content of each locus. The data were subsequently used to assess the validity of a combination of twelve loci for sable individualization. We defined twelve polymorphic loci that were easy to be amplified and genotyped. Four significant deviations from Hardy-Weinberg equilibrium were observed among the 12 loci in the three populations. The match probability of an individual from the reference populations with a random individual based on the 12 loci was 1.37 × 10−13. Using the combination of the twelve loci provides sufficient power to individualize sables considering the levels of microsatellite polymorphism observed. These loci were successfully applied to a case of sable poaching and provided valid evidence to determine the penalty. The genetic individualization of sable based on these loci might also be useful to investigate the numbers of animals in wild populations.

Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species.

Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e‐PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker‐assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.

Multiplex pyrosequencing of InDel markers for forensic DNA analysis.

The capillary electrophoresis (CE) technology is commonly used for fragment length separation of markers in forensic DNA analysis. In this study, pyrosequencing technology was used as an alternative and rapid tool for the analysis of biallelic InDel (insertion/deletion) markers for individual identification. The DNA typing is based on a subset of the InDel markers that are included in the Investigator® DIPplex Kit, which are sequenced in a multiplex pyrosequencing analysis. To facilitate the analysis of degraded DNA, the polymerase chain reaction (PCR) fragments were kept short in the primer design. Samples from individuals of Swedish origin were genotyped using the pyrosequencing strategy and analysis of the Investigator® DIPplex markers with CE. A comparison between the pyrosequencing and CE data revealed concordant results demonstrating a robust and correct genotyping by pyrosequencing. Using optimal marker combination and a directed dispensation strategy, five markers could be multiplexed and analyzed simultaneously. In this proof-of-principle study, we demonstrate that multiplex InDel pyrosequencing analysis is possible. However, further studies on degraded samples, lower DNA quantities, and mixtures will be required to fully optimize InDel analysis by pyrosequencing for forensic applications. Overall, although CE analysis is implemented in most forensic laboratories, multiplex InDel pyrosequencing offers a cost-effective alternative for some applications.

Abstract 386: Epigenome-wide association study to predict breast cancer risk in European Prospective Investigation into Cancer and Nutrition (EPIC) cohort

Abstract Aberrant DNA methylation (DNAm) in blood has been used as an epigenetic marker of cancer risk although, the significance of DNAm changes in surrogate tissues as a marker of predicting breast cancer risk remains elusive. This may be potentially accounted by the fact that there are very few study cohorts to understand the significance of DNA methyation prospectively. We examined the potential of DNAm in peripheral blood as a marker of breast cancer risk in a nested case-control cohort of European Prospective Investigation into Cancer and Nutrition (EPIC) study. The study cohort involved 451 female incident breast cancer cases and matched controls (matched for center, age, date of blood collection and menopausal status). Majority of breast cancer cases were localized (47%) and receptor positive (83.1%) while a smaller proportion of samples were metastatic (14%) and 20% of the cases were triple negative. Methylation levels were measured across 485,777 CpG sites using the Illumina HumanMethylation 450K BeadChip array. The cross-reactive probes and polymorphic CpGs were filtered during the analysis. Methylation values for all the probes thus obtained were compared between cases and matched controls using logistic regression model with adjustments for potential confounders. We found differential methylation across 185 probes (P<0.0005) and we believe that these probes may serve as potentially useful surrogate markers for identification of individuals with a high risk of breast cancer development. We are currently verifying and validating these findings in our study cohort and the findings will be discussed at the meeting. Citation Format: Srikant Ambatipudi, Veronique Chajes, Florence Le Calvez-Kelm, Cyrille Cuenin, Geoffroy Durand, Isabelle Romieu, Zdenko Herceg. Epigenome-wide association study to predict breast cancer risk in European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 386. doi:10.1158/1538-7445.AM2014-386

Development of SNP markers for individual identification and parentage test in a Japanese Black cattle population

This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers. The allelic frequencies for each marker were estimated by using PCR-RFLP in the Japanese Black population. Based on the frequency data, the estimated identity power of these markers was 2.73 x 10(-12). Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.96929 and 0.99693, respectively. This panel of SNP markers is theoretically sufficient for individual identification, and would also be a powerful tool for a parentage test in Japanese Black cattle. The markers could contribute to the management of the beef industry in Japan.

Genetic Polymorphisms in Genes Encoding Antioxidant Enzymes Are Associated With Diabetic Retinopathy in Type 1 Diabetes

OBJECTIVEOxidative stress plays an important role in the development of microangiopathic complications in type 1 diabetes. We investigated polymorphic markers in genes encoding enzymes regulating production of reactive oxygen species in association with diabetic retinopathy or diabetic nephropathy.RESEARCH DESIGN AND METHODSA total of 124 patients with type 1 diabetes were investigated in this case-control study. All subjects were matched for sex, age, and duration of diabetes. Genotyping was conducted using real-time PCR for p.Val16Ala polymorphism in the MnSOD gene and c.C−262T in the promoter region of the CAT gene. Multiplex PCR method was used for determination of GSTM1 and GSTT1 polymorphic deletions. Fluorescence-labeled PCR amplicons and fragment analysis was used for assessing the number of pentanucleotide (CCTTT)n repeats in inducible nitric oxide synthase.RESULTSA positive association of MnSOD genotype Val/Val (odds ratio [OR] 2.49, 95% CI 1.00–6.16, P = 0.045) and GSTM1–1 genotype (2.63, 1.07–6.47, P = 0.031) with diabetic retinopathy but not with diabetic nephropathy was demonstrated. Additionally, the combination of the two genotypes conveyed an even higher risk (4.24, 1.37–13.40, P = 0.009). No other investigated genetic polymorphisms were associated with either diabetic retinopathy or diabetic nephropathy.CONCLUSIONSSelected polymorphisms in genes encoding MnSOD and GSTM1 could be added to a panel of genetic markers for identification of individuals with type 1 diabetes at an increased risk for developing diabetic retinopathy.

Quantitative T2 mapping as a potential marker for the initial assessment of the severity of damage after traumatic brain injury in rat

Severity of traumatic brain injury (TBI) positively correlates with the risk of post-traumatic epilepsy (PTE). Studies on post-traumatic epileptogenesis would greatly benefit from markers that at acute phase would reliably predict the extent and severity of histologic brain damage caused by TBI in individual subjects. Currently in experimental models, severity of TBI is determined by the pressure of applied load that does not directly reflect the extent of inflicted brain injury, mortality within experimental population, or impairment in behavioral tests that are laborious to perform. We aimed to compare MRI markers measured at acute post-injury phase to previously used indicators of injury severity in the ability to predict the extent of histologically determined post-traumatic tissue damage. We used lateral fluid-percussion injury model in rat that is a clinically relevant model of closed head injury in humans, and results in PTE in severe cases. Rats (48 injured, 12 controls) were divided into moderate (mTBI) and severe (sTBI) groups according to impact strength. MRI data (T2, T2*, lesion volume) were acquired 3 days post-injury. Motor deficits were analysed using neuroscore (NS) and beam balance (BB) tests 2 and 3 days post-injury, respectively. Histological evaluation of lesion volume (Fluoro-Jade B) was used as the reference outcome measure, and was performed 2 weeks after TBI. From MRI parameters studied, quantitative T2 values of cortical lesion not only correlated with histologic lesion volume (P<0.001, r=0.6, N=34), as well as NS (P<0.01, r=−0.5, N=34) and BB (P<0.01, r=−0.5, N=34) results, but also successfully differentiated animals with mTBI from those with sTBI 70.6 ± 6.2 6.2 ms vs. 75.9 ± 2.6 ms, P<0.001). Quantitative T2 of the lesion early after TBI can serve as an indicator of the severity of post-traumatic cortical damage and neuro-motor impairment, and has a potential as a clinical marker for identification of individuals with elevated risk of PTE.

Analysis of microsatellite markers D18S70 and d20S116 in DNA isolated from dentin: Use in forensic medicine

Short tandem repeats and more specifically microsatellites represent a powerful tool in forensic medicine. In the past years, they have been extensively used in human identification and paternity testing. The aim of the present study was to analyze two microsatellite markers in the Serbian population, i.e. to determine the number of alleles and the relevant forensic parameters. DNA was isolated from teeth samples using standard proteinase K digestion and phenol/chloroform alcohol extraction. PCR products were analyzed on polyacrilamide gels and visualized by AgNO3 staining. Forensic parameters were calculated using the Cervus software. The loci D18S70 and D20S116 were analyzed on a sample of 70 unrelated, healthy adult individuals from Serbia. The number of alleles was determined and Hardy Weinberg equilibrium was confirmed for both loci. D18S70 and D20S116 demonstrated 6 and 8 alleles, respectively. The power of discrimination (PD) and the power of exclusion (PE) for the tested STR loci, D18S70 and D20S116 were 0.92 (PD), 0.41 (PE) and 0.95 (PD), 0.480 (PE), respectively. According to the presented data, D18S70 and D20S116 are most informative markers. Based on allelic frequencies and statistical parameters for forensic testing, it may be suggested that these two microsatellites represent useful markers for individual identification and parentage analysis in the Serbian population.

Microsatellite analysis in domesticated and wild Atlantic salmon ( Salmo salar L.): allelic diversity and identification of individuals

Samples of wild and domesticated salmon in Norway were genotyped at 12 microsatellite loci to compare allelic variability and investigate the potential of microsatellite markers for identification of individuals. The following loci were amplified: Ssa20, Ssa62NVH, Ssa71NVH, Ssa90NVH, Ssa103NVH, Ssa105NVH, SsaF43; Ssa20.19; Ssa13.37; SsOSL85; Ssa197; Ssa28. All domesticated strain samples displayed reduced variability compared to wild salmon. On average 58% of the allelic richness observed within the four wild stocks were present in the samples taken from domesticated strains. No systematic differences in heterozygosity were observed between samples representing the two groups. Pairwise genetic distances, as estimated by Fst values and Nei [1978] was 2–8 times higher among domesticated strains than among wild strains. Among the wild stocks, the highest genetic distances were observed between the river Neiden, located in northern Norway, and the other wild stocks located in the southwest of Norway. Assignment tests indicated that the wild and domesticated salmon could be distinguished with high precision. Less than 4% of domesticated salmon were misassigned as wild salmon, and less than 3% of wild fish were misassigned as domesticated salmon. Fish from individual domesticated strains were identified with similarly high precision. Assignment to wild salmon stocks was less accurate, with the exception of the sample taken from the river Neiden, for which 93% of the individuals were correctly assigned.

Epidemiologie (Inzidenzen, Mortalität, Überlebensraten), Risikofaktoren, Vorbeugung (Screening)

BACKGROUND: Lung cancer is currently the main cause of cancer deaths in both men and women worldwide. METHODS: Review of recent literature. RESULTS: The expected 5-year survival rate for all patients in whom lung cancer is diagnosed is 15%, compared with 61% for colon cancer, 86% for breast cancer, and 96% for prostate cancer. The 5-year survival rate for patients with potentially resectable lung cancer is significantly less than 100% (stage IA, 67%; stage IB, 57%; stage IIA, 55%; stage IIB, 39%; and stage IIIA, 23%). Since cigarette smoking is known as the main risk factor, incidence, mortality and risk of lung cancer development can be certainly reduced by means of smoking cessation as well as prevention of smoking initiation among non-smokers. Regarding chemoprevention, currently there are no agents that have been proven to be effective for preventing lung cancer. Despite the fact that data from randomised studies which would support large screening programs are still not available, mortality from lung cancer could be reduced greatly through the development of molecular markers for identification of individuals at the earliest stages of lung cancer when curative resection is feasible. CONCLUSIONS: Cigarette smoking (active or passive) represents the leading risk factor and the main cause for lung cancer.

개의 친자감정을 위한 Microsatellite DNA 다형성 분석

ABSTRACT This study was carried out to investigate a usefulness of the microsatellite DNA markers for individual identification and parentage verification in three dog breeds. A total of 59 random dog (31 Chiwawa, 20 Poongsan, 8 Labrador Retriever) samples were genotyped by using 14 markers (Chiwawa dog), 16 markers (Poongsan dog), and 12 markers (Labrador Retriever dog) among the 17 international standard markers (PEZ1, 3, 5, 6, 8, 10, 11, 12, 13, 15, 16, 17, 20, 21, FHC2010, FHC2054 and FHC2079), respectively. The number of alleles per locus varied from 4 to 14 with a mean value of 6.07 in Chiwawa dog, 2 to 9 with a mean of 4.75 in Poongsan dog, and 3 to 5 with a mean of 4.00 in Labrador Retriever dog. Observed heterozygosity was ranged 0.419q0.968 (mean 0.755), 0.300q0.950 (mean 0.597) and 0.125q0.750 (mean 0.604), and expected heterozygosity was ranged 0.432q0.883 (mean 0.711), 0.262q0.817 (mean 0.559) and 0.425q0.808 (mean 0.660) in these three dog breeds. PIC value was ranged 0.397q0.856 (mean 0.659), 0.222q0.772 (mean 0.503) and 0.354q0.717 (mean 0.563) in these three dog breeds. Of the 17 markers, PEZ1, PEZ3, PEZ6, PEZ10, PEZ12 loci, PEZ1, PEZ6, PEZ13 loci, and PEZ8, PEZ12 loci have relatively high PIC value (
%0.7) in Chiwawa dog, Poongsan dog and Labrador Retriever dog, respectively. The exclusion probability was ranged 0.240q0.741, 0.111q0.616, and 0.198q0.529, and the combination of microsatellite loci was 0.9999, 0.9991, and 0.9968 in Chiwawa dog, Poongsan dog and Labrador Retriever dog, respectively. These results can give basic information for developing parentage verification and individual identification system in these three dog breeds.(

Validation of SNPs as markers for individual identification

Nowadays, the DNA markers used for individual identification in forensic science are on the one hand based on repeat sequences (STR and VNTR) on genomic DNA, and on the other hand based on the mitochondrial hypervariable regions 1 and 2. An alternative to these classical markers could be single-nucleotide polymorphisms (SNPs), as they present advantages over them. Even if most SNPs are biallelic and, therefore, of limited discriminatory value, a vast number of those loci exist and are being catalogued at a rapid rate. Furthermore, those markers have a sex-unspecific transmission, are less subjects to mutations as they can be found in coding regions of DNA and their detection and analysis are relatively easy to achieve. Finally, the analysed DNA sequence is much shorter than the one used for STR research, and SNP profiles could have an application in anthropology and legal medicine where samples are old and often degraded. The aim of this study is the selection of 11 informative SNPs, i.e., conserved, phenotypically not expressed and represented at high frequencies in populations, their analysis by sequencing and the confirmation of their mendelian transmission. The principle of this method is compatible with different SNP analysis platforms (i.e., pyrosequencing, MALDI-TOF MS, SnaPShot, etc.) and could allow the achievement of a genetic profile specific for an individual in an extremely short time and at low costs. The number of SNPs present on human genome being vast, the list of the selected ones could be even longer.

DIFFERENTIAL SENSITIVITY AMONG 3 HUMAN SUBPOPULATIONS IN RESPONSE TO 4-NITROQUINOLINE-1-OXIDE AND TO BLEOMYCIN

An assay employing the UV-mimetic mutagen 4-nitroquinoline-1-oxide (4NQO) to estimate a person's UV-sensitivity was developed. This sensitivity may be translated into an individual's susceptibility to acquire cutaneous malignancies. We used cytogenetic recordings on cultured lymphocytes from 103 normal individuals, 62 melanoma patients, and 71 patients with head and neck cancer. The frequency of chromosome damage (chromatid breaks) caused by exposure to 4NQO was used to measure sensitivity. Preliminary results showed that a significantly higher proportion of melanoma patients was 4NQO sensitive compared to the other two groups, whose 4NQO sensitivity was statistically not different. Although a number of theoretical and technical problems remain to be resolved and a great deal of additional information (especially clinical and epidemiological) is needed, it appears that 4NQO sensitivity may be effectively employed as a biological marker for identification of individuals at risk for melanoma (and possibly other cutaneous neoplasms as well).

Serum Apoprotein (ApoA1 and ApoB) in Myocardial infarction

30 diagnosed cases (Male26, Female 4) of MI (myocardial infarction) with the mean age of 55.5±9.8 years (range 40- 70 years) were included in a case control study to evaluate their apoprotein status. Serum apoA1 and apoB were measured and compared with those of age and sex matched healthy control subjects. Mean serum apoA1 concentration found significantly low in MI cases (91.84± 11.2 mg/dl) compared to control ( 123.2±10.5 mg/dl) and that of apoB found significantly high in MI cases( 135.3± 23.0 mg/dl ) compared to control (66.2±10.0 mg/dl).Serum apoB/apoA1 ratio of MI cases (1.49±0.3) also found significantly higher than that of control (0.54±0.1) .Since the serum apoA1 and apoB concentration stand for relatively more comprehensive measure of antiatherogenic and atherogenic potential respectively rather than the traditional lipid profile ; measurement of this apoprotein and their ratio may be more robust and specific marker for identification of individuals at risk of MI even in individuals with normal traditional lipid profile. Key word: ApoA1, ApoB, MI DOI: 10.3329/jbcps.v26i2.4181 J Bangladesh Coll Phys Surg 2008; 26: 62-66