Calculation of Likelihood Ratios for Incest Cases Using IBD Patterns.

OBJECTIVES: To calculate the likelihood ratios of incest cases using identity by descent (IBD) patterns. METHODS: The unique IBD pattern was formed by denoting the alleles from the members in a pedigree with a same digital. The probability of each IBD pattern was obtained by multiplying the prior probability by the frequency of non-IBD alleles. The pedigree likelihoods of incest cases under different hypotheses were obtained by summing all IBD pattern probabilities, and the likelihood ratio(LR) was calculated by comparing the likelihoods of different pedigrees. RESULTS: The IBD patterns and the formulae of calculating LR for father-daughter incest and brother-sister incest were obtained. CONCLUSIONS: The calculations of LR for incest cases were illustrated based on IBD patterns.

Two loci concurrent mutations in non-exclusion parentage cases using 19 STR profiles.

Two loci concurrent mutations in non-exclusion paternity case were reported based on 19 STR loci available from Goldeneye™ DNA ID System 20A (Peoplespot, Beijing, China). When 9508 family trios with Paternity index (PI) threshold of >10,000 was analyzed, 14 families show mutations at two loci. The paternity was confirmed by using an additional 19 STR markers. When the probability of occurrence of two mutations was compared with the expected probability deduced from binomial model, the observed mutational probability was significantly larger than the expectation. However, the characteristics of mutations agree with those reported previously. Our result indicates that larger samples is still need to estimate mutation rates accurately and reveal the relationship between mutations with multiple loci and the characterization of human mutations based on microsatellites.

Population structure of Han nationality in Central-Southern China.

Knowledge of population structure is very important for forensic genetics. However, the population substructure in Central-Southern China Han nationality has still not been fully described. In this study, we investigated the genetic diversity of 15 forensic autosomal STR loci from 6879 individuals in 12 Han populations subdivided by administrative provinces in Central-Southern China. The statistical analysis of genetic variation showed that genetic differentiation among these populations was very small with a Fst value of 0.0009. The Discriminant Analysis of Principal Components (DAPC) showed that there were no obvious population clusters in Central-Southern China Han population. In practice, the population structure effect in Central-Southern China Han population can be negligible in forensic identification and paternity testing.

Population data and mutation rates of 19 STR loci in seven provinces from China based on Goldeneye™ DNA ID System 20A.

Short tandem repeat (STR) analysis is a primary tool in forensic casework. Population data and mutation rates of STRs are very important for paternity testing and forensic genetics. However, the population data and mutation rates of STRs in Han nationality based on large samples have still not been fully described in China. In this study, the allelic frequencies, forensic parameters, and mutation rate of 19 STR loci (D19S433, D5S818, D21S11, D18S51, D6S1043, D3S1358, D13S317, D7S820, D16S539, CSFIPO, PentaD, vWA, D8S1179, TPOX, Penta E, TH01, D12S391, D2S1338, and FGA) based on the Goldeneye™ DNA ID System 20A in Southern China Han nationality among seven provinces were investigated. Furthermore, population stratification of Southern China Han nationality among seven provinces was established. The multidimensional scaling (MDS) plot based on genetic distances (Fst) showed that the studied populations can be clustered into two major groups. However, relationships among populations were weak (Fst < 0.0043). A total of 376 cases of mutation were detected from the 19 selected loci in 15,396 meioses. The average mutation rate for the 19 loci was estimated to be 1.3 × 10-3 per meiosis. The mutation was mainly single step; the paternal mutation rate was higher than the maternal; and paternal mutation rate increases with paternal age.

Potential of 13 linked autosomal short tandem repeat loci in pairwise kinship analysis.

In this study, a panel of 13 STR loci locate on chromosome 3, 4, and 17 (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2404, D4S2364, AC001348A, AC001348B, D17S975, and D17S1294) were assessed for pairwise kinship analysis. Map distances between these STR loci ranged from 0.07 cM to 97.03 cM. The population genetic study of Chinese Han population showed that linkage disequilibrium exists in two clusters of closely linked markers (D4S2404-D4S2364 and D17S975-D17S1294), in which the recombination fractions were 0.0026 and 0.0001, respectively. The recombination fractions derived from the Rutgers Map for the closely linked markers (genetic distance < 0.5 cM) were significant underestimates in comparison to those of direct observation of STR transmissions in families. When effect of linkage on pairwise kinship testing was evaluated by comparing likelihood ratio (LR) values taking linkage into account, overall LR values increased. But extremely low LRs were also observed. Finally, the power of the 13 STR loci to discriminate relationship among full-sibs, half-sibs, grandparent-grandchild, uncle-niece, and unrelated pairs was assessed with a category fraction. The results showed that about 72.64% of full-sib pairs and about 82.84% of unrelated pairs could be classified correctly. But the category fractions of second-degree relationships drastically reduced to 7.34-35.48%. If only pairs of grandparent-grandchild, half-sibs, and uncle-niece were distinguished, the category fraction was 0.5512, 0.1147, and 0.4362, respectively. Our study results demonstrated that linked STRs were helpful to differentiate the most frequent relationships in pairwise kinship analysis.

Genetic polymorphism of 22 autosomal STR markers in a Han population of Southern China.

Population genetic data and forensic statistics of 22 autosomal short tandem repeat (STR) loci (D1S1656, D2S1338, D3S3045, D4S2366, D5S2500, D6S477, D7S3048, D8S1132, D9S925, D10S1435, D11S2368, D12S391, D13S325, D14S608, D15S659, D16S539, D17S1290, D18S535, D19S253, D20S470, D21S1270 and GATA198B05) were determined for a sample of 515 unrelated individuals from Han population in Southern China. The expected heterozygosity and the discrimination power varied from 0.7358 to 0.8733 and 0.8915 to 0.9702, respectively. The probability of excluding an unrelated man as the true father (assuming no background relatedness in the population) for trios and for duos ranged from 0.5126 to 0.7415 and 0.3331 to 0.5864, respectively. The studied STRs appear to provide a significant improvement in the statistical power of kinship analysis.

TMEM16A overexpression contributes to tumor invasion and poor prognosis of human gastric cancer through TGF-ß signaling.

TMEM16A is a newly identified calcium activated chloride channel, and has been reported to be overexpressed by various solid malignant cancers to promote proliferation and invasion, yet little is known about its role in gastric cancer(GC). Therefore, we investigated the role of TMEM16A in GC and its clinical significance by a retrospective analysis of 367 GC patients, and in vitro study was performed for validation and underlying molecular mechanism.TMEM16A was significantly upregulated and amplified in GC tissues, and its overexpression was positively correlated with disease stage, negatively with patient survival and identified as an independent prognostic factor for patient outcome. A negative correlation between TMEM16A and E-cadherin was found in 367 GC specimens. TMEM16A silencing significantly decreased calcium activated chloride currents, impaired TGF-ß secretion, reduced E-cadherin expression, and inhibited the migration and invasion without affecting proliferation of GC cells (AGS and BGC-823). Supplement of TGF-ß reverted the effects of TMEM16A silencing on E-cadherin expression, cell migration and invasion.In conclusion, TMEM16A promotes invasion and metastasis in GC, and might be a novel prognostic biomarker and potential therapeutic target in the treatment of GC.

Genetic polymorphism of 13 non-CODIS STR loci in three national populations from China.

The aim of this study was to investigate a 13 non-CODIS STR loci database using three national populations from China. A new multiplex PCR system that simultaneously amplified 13 loci in the same PCR reaction was developed. This multiplex system included the 13 STR markers (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2364, D4S2404, AC001348A, AC001348B, D17S975, and D17S1294), which were successfully analyzed by using 441 DNA samples from three national populations in China (154 Mongol, 177 Kazakh, and 110 Uigur). Allele frequencies and mutation rates of the 13 non-CODIS STR loci were investigated. A total of 4-10 alleles at each locus were observed and altogether 84, 88, and 87 alleles for the all selected loci were found in the Mongol, Kazakh, and Uigur, respectively. Eight mutations were detected from the 13 selected loci in 9880 meioses in kinship cases. These results indicate that this multiplex system may provide significant polymorphic information for kinship testing and relationship investigations.

Recombination analysis of autosomal short tandem repeats in Chinese Han families.

Recombination fractions between forensic STRs can be extrapolated from the International HapMap Project, but the concordance between recombination fractions predicated from genetic maps and derived from observation of STR transmissions in families is still ambiguous for autosomal STRs because of limited family studies. Therefore, the main goal of this study is to compare recombination fractions estimated by pedigree analysis with those derived from HapMap phase SNP data. Genotypes of nine autosomal STR pairs (TPOX-D2S1772, D5S818-CSF1PO, D7S3048-D7S820, D8S1132-D8S1179, TH01-D11S2368, vWA-D12S391, D13S325-D13S317, D18S51-D18S1364, and D21S11-PentaD) from 207 two-generation families with two to five children (the number of families with five, four, three, and two children was 2, 3, 20, and 182, respectively) were used to analyze the recombination. The linkage analysis showed that significant linkage was observed at six STR pairs (D5S818-CSF1PO, D8S1132-D8S1179, TH01-D11S2368, vWA-D12S391, D13S325-D13S317, and D18S51-D18S1364) with genetic distances <36.22 cM in HapMap. Their recombination fractions calculated from family data were very close to those derived from HapMap. However, three STR pairs of TPOX-D2S1772, D7S3048-D7S820, and D21S11-PentaD showed no significant linkage with genetic distances from 43.38 to 91.49 cM. Our results indicate that recombination fractions extrapolated from HapMap can provide a substitute if empirical data are unavailable for the linkage STR pair with a genetic distance spanned <36.22 cM.

X chromosomal recombination--a family study analyzing 26 X-STR Loci in Chinese Han three-generation pedigrees.

The aim of this study is to investigate genetic linkage and recombination fractions of 26 X chromosomal (X-STR) loci with two multiplex PCR systems (MX15-STR and MX12-STR). MX15-STR (including DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079) and MX12-STR (including DXS6854, DXS9902, DXS6800, GATA172D05, DXS7423, HPRTB, DXS6807, DXS6803, DXS6804, DXS6799, DXS8378, and DXS8377) were successful analyzed on 206 two-generation families with two or more children and 33 three-generation families with 72 grandsons. Segregation analysis and calculation of recombination fractions between pairs of markers were performed. Linkage analysis of pairs of markers showed that there existed significant linkage (maximum LOD scores >2.0) within the physical distance of 48.5 Mb. Recombination events could be observed within the clusters of closed linked makers spanning <1.0 Mb. These results indicate that close cluster X-STRs used and recombination fractions of the selected loci will be very useful for biostatistical calculations in complex kinship analysis.

Allele and Haplotype Diversity of 26 X-STR Loci in Four Nationality Populations from China.

BACKGROUND: Haplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis, especially when short tandem repeats (STR) fail to resolve uncertainty in relationship analysis. STR located on the X chromosome show stronger linkage disequilibrium compared with autosomal STR. So, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific. METHODOLOGY AND FINDINGS: Twenty-six X-STR loci including six clusters of linked markers DXS6807-DXS8378-DXS9902(Xp22), DXS7132-DXS10079-DXS10074-DXS10075-DXS981 (Xq12), DXS6801-DXS6809-DXS6789-DXS6799(Xq21), DXS7424-DXS101-DXS7133(Xq22), DXS6804-GATA172D05(Xq23), DXS8377-DXS7423 (Xq28) and the loci DXS6800, DXS6803, DXS9898, GATA165B12, DXS6854, HPRTB and GATA31E08 were typed in four nationality (Han, Uigur, Kazakh and Mongol) samples from China (n = 1522, 876 males and 646 females). Allele and haplotype frequency as well as linkage disequilibrium data for kinship calculation were observed. The allele frequency distribution among different populations was compared. A total of 5-20 alleles for each locus were observed and altogether 289 alleles for all the selected loci were found. Allele frequency distribution for most X-STR loci is different in different populations. A total of 876 male samples were investigated by haplotype analysis and for linkage disequilibrium. A total of 89, 703, 335, 147, 39 and 63 haplotypes were observed. Haplotype diversity was 0.9584, 0.9994, 0.9935, 0.9736, 0.9427 and 0.9571 for cluster I, II, III, IV, V and VI, respectively. Eighty-two percent of the haplotype of cluster IIwas found only once. And 94% of the haplotype of cluster III show a frequency of <1%. CONCLUSIONS: These results indicate that allele frequency distribution for most X-STR loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation. So it is necessary to obtain allele frequency and haplotypes data of the linked loci for forensic application.

Development of multiplex PCR system with 15 X-STR loci and genetic analysis in three nationality populations from China.

The aim of this study is to develop a new multiplex PCR system that simultaneously amplifies the 15 X-chromosome short tandem repeats (X-STRs) loci in the same PCR reaction, and to obtain the 15 X-STR loci database in three nationality populations from China. This multiplex system includes DXS7133, DXS6801, DXS981, DXS6809, DXS7424, DXS6789, DXS9898, DXS7132, GATA165B12, DXS101, DXS10075, DXS6800, GATA31E08, DXS10074, and DXS10079, which were successfully analyzed on 1251 DNA samples (670 males and 581 females) from Guangdong Han population, Xinjiang Uigur and Kazakh. The allele frequencies and mutation rates of the 15 loci were investigated, and the allele frequency distribution among different populations was compared. A total of 6-17 alleles for each locus were observed and altogether 170 alleles for all the selected loci were found. Thirteen cases with mutation of the above loci were detected in 11,850 meioses. Pairwise comparisons of the allele frequencies distribution showed significant differences in most loci among different populations. The results indicate that this multiplex system may provide high polymorphism information for kinship testing and relationship investigations, and it is necessary to gain allele frequency and mutation rate of different population for forensic application.

Development and population study of the 12 X-STR loci multiplexes PCR systems.

To develop a multiplex polymerase chain reaction (PCR) system with 12 X-chromosomal short-tandem repeat (X-STR) loci and to investigate their polymorphism and linkage and/or independence, the 12 loci (DXS6807, DXS8378, DXS9902, DXS6800, DXS6803, DXS6799, DXS6804, GATA172D05, DXS6854, HPRTB, DXS8377, and DXS7423) were simultaneously analyzed in 1,005 unrelated individuals (574 males and 431 females) from Guangdong Han individuals and Kazakh populations living in China. The allele frequencies and mutation rates were investigated. Allele frequency distribution among different populations was compared. Haplotypes of linkage disequilibrium markers (DXS6807-DXS8378-DXS9902) and linked markers (DXS6804-GATA172D05 and DXS8377-DXS7423) were also reported. A total of 117 alleles, ranging from five to 20 for each locus, were observed in our selected populations. Eight cases with mutation of the selected loci were detected in 9,480 meioses. Pairwise comparisons of allele frequencies distribution showed statistically significant differences at most loci among different populations. Haplotype diversity of linked markers was 0.9404-0.9694. The results indicated that this multiplex system is very useful for forensic analysis and may be complementarities for X-12 kits or X-8 kits in forensic case.

Neural correlates of feigned memory impairment are distinguishable from answering randomly and answering incorrectly: an fMRI and behavioral study.

Previous functional magnetic resonance imaging (fMRI) studies have identified activation in the prefrontal-parietal-sub-cortical circuit during feigned memory impairment when comparing with truthful telling. Here, we used fMRI to determine whether neural activity can differentiate between answering correctly, answering randomly, answering incorrectly, and feigned memory impairment. In this study, 12 healthy subjects underwent block-design fMRI while they performed digit task of forced-choice format under four conditions: answering correctly, answering randomly, answering incorrectly, and simulated feigned memory impairment. There were three main results. First, six areas, including the left prefrontal cortex, the left superior temporal lobe, the right postcentral gyrus, the right superior parietal cortex, the right superior occipital cortex, and the right putamen, were significantly modulated by condition type. Second, for some areas, including the right superior parietal cortex, the right postcentral gyrus, the right superior occipital cortex, and the right putamen, brain activity was significantly greater in feigned memory impairment than answering randomly. Third, for the areas including the left prefrontal cortex and the right putamen, brain activity was significantly greater in feigned memory impairment than answering incorrectly. In contrast, for the left superior temporal lobe, brain activity was significantly greater in answering incorrectly than feigned memory impairment. The results suggest that neural correlates of feigned memory impairment are distinguishable from answering randomly and answering incorrectly in healthy subjects.

Development of the nine X-STR loci typing system and genetic analysis in three nationality populations from China.

This study is to develop a new multiplex polymerase chain reaction (PCR) system that simultaneously amplifies the nine X-chromosome short tandem repeats loci in the same PCR reaction, and to explore their polymorphism and mutation rate among three nationality populations from China. These loci included DXS6854, DXS9902, DXS6809, GATA172D05, HPRTB, DXS7423, DXS6807, DXS8378, and DXS8377. The samples of 890 (484 males and 406 females) unrelated individuals from Guangdong Han population, Xinjiang Uigur, and Inner-Mongolia Mongol were successfully analyzed using this multiplex system. The allele frequencies and mutation rates of the nine loci were investigated, and the comparison of allele frequency distribution among different populations was performed. There were 87 alleles for all the loci, and six to 18 alleles for each locus observed by our new multiplex PCR system. Polymorphism information content was 0.4998-0.9101, and power of discrimination in females was 0.6518-0.9846. Five cases with mutation of above loci were detected in 5,310 meioses. Pair-wise comparisons of allele frequencies distribution showed significant differences for most loci among different populations. Our results indicate that this multiplex system is very useful for identification analysis, and that the information about polymorphism and mutation rate is necessary for forensic application in three nationality populations from China.

Genetic data of nine non-CODIS STRs in Chinese Han population from Guangdong Province, Southern China.

Nine non-combined DNA index system tetranucleotide short tandem repeat (STR) loci D2S1772, D6S1043, D7S3048, D8S1132, D11S2368, D12S391, D13S325, D18S1364, and GATA198B05 were amplified in a multiplex polymerase chain reaction system. The distribution of alleles of the nine STRs was reported from a Chinese Han population in Guangdong Province, Southern China. The combined power of exclusion in trios and duos for the nine loci was 0.999981 and 0.999025, respectively. Mutation rates range from 0 to 0.005618. Pairwise analysis of linkage disequilibrium, which included PowerPlex 16 System loci, did show statistically significant deviation from independence even though loci locate on the same chromosomes. The nine STRs are highly informative and suitable to extend the results obtained with other STRs commonly analyzed for difficult paternity and kinship analysis.

[Calculation of the avuncular index].

OBJECTIVE: To introduce the method of avuncular index (AI) calculation. METHODS: Identity by decent coefficient, coancestry coefficient and AI law were employed in identification of uncle-niece relationship, when autosomal STR loci were detected to determine controversial uncle-niece relationship. RESULTS: The results of AI calculation were coincidental using identity by descent coefficien, coancestry coefficient and AI law. CONCLUSION: The results are coincidental using three methods in the different situations. AI index is higher with participation of children's mother.

Genetic analysis of the 10 ChrX STRs loci in Chinese Han nationality from Guangdong province.

This study is to explore the polymorphic nature of X-Chromosome short tandem repeats (ChrX STRs) loci, and to determine its application in kinship tests for forensic cases. A new fluorescent multiplex PCR that simultaneously amplifies the 10 ChX STRs loci in the same PCR reaction had been set up. DXS7132, DXS981, DXS6801, DXS6809, DXS6789, DXS7424, DXS101, DXS7133, GATA165B12 and GATA31E08 were analyzed in a sample of 511 (399 males and 112 females) unrelated individuals from Guangdong Han nationality in China. One hundred and one alleles were observed in all the loci. Here, we investigated the allele frequencies and mutation rates of the ten loci, and then made the comparison of allele frequencies distribution among different populations. The results show the ten loci in the multiplex systems may provide high polymorphism information for kinship testing and relationship investigations, and it is necessary to gain allele frequency and mutation rate of different population for forensic application.

[A new method for calculating paternity index].

OBJECTIVE: To introduce a new method for calculating the paternity index (PI). METHODS: Assuming that each allele from parents has undergone a transition before it segregates and transmits to child. The transition probability is 1 when parent allele is the same as child's, the transition probability is 0 when parent allele is different from the child's. Every allele has a transmission probability with 0.5. Base on these theories, it is easy to gain the probability that child inherits an allele from the alleged father or mother. Thus, the X value (numerator) and Y value (denominator) of PI formula can be calculated, as unknown man provide an allele for child with the allele frequency. RESULTS: A general formula that calculated the PI for trios, duos and missing child cases was deduced. CONCLUSION: The new method is practical in all kinds of forensic paternity case.