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.

Deletions and duplications of 42 Y chromosomal short tandem repeats in Chinese Han population.

Genotypes of 42 Y chromosome STR (Y-STR) loci were analyzed for a sample of 1420 unrelated males and 1160 father-son pairs from a Chinese Han population. Deletions of Y-STR loci were detected at DYS389I, DYS389II, DYS437, DYS446, DYS447, DYS448, and DYS557 loci. The most common deletion occurred at DYS448 and DYS557 with a frequency of 0.0056 and 0.0035, respectively. On the other hand, duplications of alleles were observed at DYF387S1a/b, DYS385a/b, DYS460, DYS527a/b, DYS459a/b, and DYS557 loci. The DYF387S1a/b, DYS527a/b, and DYS385a/b showed the highest duplicated frequencies of 0.0148, 0.0134, and 0.0099, respectively. The Y-STRs located on palindromes significantly exhibited more deletions or duplications than those non-palindromic loci. Also, duplications were more frequent than deletions. Hence, deletions or duplications of Y-STRs related to their positions on the Y chromosome. All the 52 deleted or duplicated events occurred in the two-generation families inherited stably. Furthermore, the deletions may show the Chinese Han population specificity, but the duplications may not have a similar phenomenon. Our results will be helpful to correct interpretation of the genetic profile of Y-STR loci in forensic casework.

Population structure of Han population in China revealed by 41 STR loci.

Background: Currently, the Han population in China may be comprised of different genetic groups due to geographic, cultural and economic factors. Understanding population structure is very important for forensic purposes. However, knowledge of the genetic substructure within the whole Han population in China is still limited.Aim: This study is designed to ascertain the genetic structure of the Han population in China through genetic data from autosomal short tandem repeats (STRs).Subjects and methods: A set of 41 STR markers were analysed in 8725 unrelated Han Chinese males from the seven geographic regions of Northeast, North, East, Central, South, Southwest and Northwest in mainland China. Allele frequencies and F-statistics were estimated. Principal coordinate analysis (PCoA), phylogenetic analyses, analysis of molecular variance (AMOVA) and discriminant analysis of principal components (DAPC) were performed to explore the population structure.Results: Rare alleles that have not been observed in previous samples were detected. The small overall Fst values (0.0008), AMOVA and DAPC indicated that there is no population structure in Han Chinese. However, the PCoA and phylogenetic tree disclose a genetic differentiation pattern from north to south.Conclusions: There is no apparent population substructure in the Han population in China. However, genetic distances among the Han populations correlate with geographic locations.

Population genetic data of Investigator HDplex markers in Han population from Southern China.

Allele frequencies and forensic statistical parameters for 12 STRs contained in the Investigator HDplex Kit (D2S1360, D3S1744, D4S2366, D5S2500, SE33, D6S474, D7S1517, D8S1132, D10S2325, D12S391, D18S51, and D21S2055) were estimated from a sample of 503 unrelated individuals from the Guangdong Han population of South China. No significant departure from the Hardy-Weinberg equilibrium or genetic linkage disequilibrium was observed (after Bonferroni correction). The expected heterozygosity ranged from 0.6411 to 0.9414. The allele frequencies in Guangdong Han significantly differed from that in Shanghai Han, Korea, Northern Italian, Swedish, Dutch, Somalia, and Argentinean populations at 2 to 12 loci. The markers included in the kit have highly polymorphic information that could be used for forensic DNA analysis as potential tools for differentiating Han population from other populations in the world.

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.

Mutation rates at 42 Y chromosomal short tandem repeats in Chinese Han population in Eastern China.

Mutation analysis of 42 Y chromosomal short tandem repeats (Y-STRs) loci was performed using a sample of 1160 father-son pairs from the Chinese Han population in Eastern China. The results showed that the average mutation rate across the 42 Y-STR loci was 0.0041 (95% CI 0.0036-0.0047) per locus per generation. The locus-specific mutation rates varied from 0.000 to 0.0190. No mutation was found at DYS388, DYS437, DYS448, DYS531, and GATA_H4. DYS627, DYS570, DYS576, and DYS449 could be classified as rapidly mutating Y-STRs, with mutation rates higher than 1.0 × 10-2. DYS458, DYS630, and DYS518 were moderately mutating Y-STRs, with mutation rates ranging from 8 × 10-3 to 1 × 10-2. Although the characteristics of the Y-STR mutations were consistent with those in previous studies, mutation rate differences between our data and previous published data were found at some rapidly mutating Y-STRs. The single-copy loci located on the short arm of the Y chromosome (Yp) showed relatively higher mutation rates more frequently than the multi-copy loci. These results will not only extend the data for Y-STR mutations but also be important for kinship analysis, paternal lineage identification, and family relationship reconstruction in forensic Y-STR analysis.

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.

Analysis of linkage and linkage disequilibrium for syntenic STRs on 12 chromosomes.

The purpose of this study is to evaluate allelic association and linkage of 18 adjacent syntenic short tandem repeat (STR) pairs form out of 30 markers located on 12 different autosomes. Linkage disequilibrium was tested by using the unknown gametic phase genotypes and phased haplotypes from 290 unrelated individuals from Chinese Han population. Genetic linkage analysis between syntenic STRs was performed based on 145 two-generation families which involved 628 meioses. The results showed no significant linkage disequilibrium at any STR pairs and independent inheritance between syntenic STR pairs was indicated. Significant linkage (maximum logarithm of odd (LOD) scores >3.0) was found in 6 out of the 18 adjacent syntenic STR pairs (D1S1627-D1S1677, CSF1PO-D5S818, D6S1017-D6S1043, D6S1043-D6S474, D12S391-vWA, and D19S253-D19S433). These significant linkage marker pairs had a genetic distance ranged from 11.94 to 41.33 cM deduced from HapMap. When recombination fractions determined in families were compared to those derived from Kosambi mapping function based on HapMap data, the latter may have an overestimation. In summary, our results demonstrated that product rule included syntenic STRs can be used for unrelated individual profile probability and the recombination fraction based on family data was superior to the estimation from HapMap for kinship analysis.

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.

Population genetic data of the NGM SElect STR loci in Chinese Han population from Zhejiang region, China.

Genetic variations of the 17 NGM SElect STR loci in Chinese Han samples from the Zhejiang region were analyzed. The results show that the NGM SElect is a highly genetic informative system in Zhejiang Han, and this population shows quite different genetic data from other major populations in the world with the exception of the Fujian Han.

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.