Actual mutational research of 19 autosomal STRs based on restricted mutation model and big data.

Short tandem repeat (STR) markers have been widely used in forensic paternity testing and individual identification, but the STR mutation might impact on the forensic result interpretation. Importantly, the STR mutation rate was underestimated due to ignoring the "hidden" mutation phenomenon in most similar studies. Considering this, we use Slooten and Ricciardi's restricted mutation model based on big data to obtain more accurate mutation rates for each marker. In this paper, the mutations of 20 autosomal STRs loci (D3S1358, D1S1656, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D6S1043, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, and FGA; The restricted model does not include the correction factor of D6S1043, this paper calculates remaining 19 STR loci mutation rates) were investigated in 28,313 (Total: 78,739 individuals) confirmed parentage-testing cases in Chinese Han population. As a result, total 1665 mutations were found in all loci, including 1614 one-steps, 34 two-steps, 8 three-steps, and 9 nonintegral mutations. The loci-specific average mutation rates ranged from 0.00007700 (TPOX) to 0.00459050 (FGA) in trio's and 0.00000000 (TPOX) to 0.00344850 (FGA) in duo's. We analyzed the relationship between mutation rates of the apparent and actual, the trio's and duo's, the paternal and maternal, respectively. The results demonstrated that the actual mutation rates are more than the apparent mostly, and the values of µ1"/µ2"(apparent) are also greater than µ1/µ2 (actual) commonly (µ1", µ1; µ2", µ2 are the mutation rates of one-step and two-step). Therefore, the "hidden" mutations are identified. In addition, the mutations rates of trio's and duo's, the paternal and maternal, exhibit significant difference. Next, those mutation data are used to do a comparison with the studies of other Han populations in China, which present the temporal and regional disparities. Due to the large sample size, some rare mutation events, such as monozygotic (MZ) mutation and "fake four-step mutation", are also reported in this study. In conclusion, the estimation values of actual mutations are obtained based on big data, they can not only provide basic data for the Chinese forensic DNA and population genetics databases, but also have important significance for the development of forensic individual identification, paternity testing and genetics research.

[Genetic variability and phylogenetic analysis of 39 short tandem repeat loci in Beijing Han population].

In this study, we studied the genetic polymorphisms of short tandem repeat (STR) loci from 13 CODIS and 26 non-CODIS system in Beijing Han population for the first time, and established a database of 39 STR loci whose forensic parameters were further evaluated. Our results demonstrated no significant deviation from the Hardy-Weinberg equilibrium of 39 STR loci and no pairwise linkage disequilibrium between them. The power of discriminations, expected heterozygosity, polymorphic information content, and power of exclusion of 39 STR loci ranged from 0.7740-0.9818, 0.6000-0.9350, 0.5317-0.9047 and 0.2909-0.8673. The cumulated discrimination power and cumulative probability of exclusion were 0.999999999999999999999999999999999999999964971 and 0.999999999973878, respectively. Moreover, the genetic distance was calculated based on allele frequency and phylogenetic tree was built using STR loci data from Beijing Han and other 11 Chinese ethnic groups.This study provides important basic data for Chinese forensic DNA database and population genetics database, and has important significance in carrying out forensic individual identification, paternity testing, and population genetic study.

[Analysis and Discussion on Calculating Likelihood Ratio of DNA Mixture].

OBJECTIVE: To analyze and discuss four methods of calculating likelihood ratio of DNA mixture. METHODS: In the case with CNAS-T0757 proficiency testing in 2013, the likelihood ratios were calculated and compared among four methods, including unrestricted combinatorial method, Clayton's method, p2 principle method, and recommendations from ISFG. RESULTS: The likelihood ratios were maximum by Clayton's method and recommendations from ISFO, followed by result of the unrestricted combinational method. The minimum likelihood ratio was obtained by p2 principle. CONCLUSION: The unrestricted combinational method could give fUrthest consideration to both information preservation and appraiser protection.

[Genetic polymorphisms of 16 non-CODIS STR loci in Beijing Han population].

OBJECTIVE: To investigate the genetic polymorphisms of 16 non-CODIS loci (D6S477, D22-GATA198B05, D15S659, D8S1132, D3S3045, D17S1290, D14S608, D2S441, D18S535, D13S325, D10S1435, DlS2368, DIS1656, D7S3048, D10S1248 and D19S253) in Beijing Han population. METHODS: The DNA of 300 unrelated individuals in Beijing Han population were PCR amplified using GoldeneyeM DNA identification system 18NC kit, and the PCR products were analyzed by electrophoresis through 3130XL genetic analyzer. The fragment sizes of alleles were taken subsequently by GeneMapper v3.2. RESULTS: The distributions of genotype frequencies of 16 non-CODIS STR loci in Beijing Han population satisfied the Hardy-Weinberg equilibration. The population genetic parameters were obtained as followings: heterozygosity was 0.677-0.873; discrimination power, 0.890-0.967; probability of paternity exclusion, 0.393-0.741; and polymorphism information content, 0.706-0.853. CONCLUSION: These 16 non-CODIS STR loci show great genetic polymorphisms in Beijing Han population, and are useful for the research of population genetics and forensic application.

[A new method of identifying the peripheral blood and the menstrual blood].

OBJECTIVE: To explore the tissue-specific gene expressions of the peripheral blood and the menstrual blood, and to search some specific factors to establish an effective method for identifying the peripheral blood and the menstrual blood. METHODS: The specific products of the peripheral blood and the menstrual blood were detected by RT-PCR and separated by electrophoretic technology. RESULTS: Beta-spectrin (SPTB) as one specific marker of peripheral blood and 18S rRNA as a kind of the housekeeping gene were expressed in both the peripheral blood and the menstrual blood. However, matrix metalloproteinase 7 (MMP7) as one specific marker of menstrual blood and human beta defensin 1 (HBD1) as one specific marker of vaginal discharge were only found in the menstrual blood. CONCLUSION: There are differences of specific gene expressions between the peripheral blood and the menstrual blood. They could be accurately distinguished from each other by using the combination of fluorescence technology and RT-PCR to detect the specific identification of mRNA.

[Application and progress of RNA in forensic science].

With the development of molecular biology, the evidences of genetics has been used widely in forensic sciences. DNA technology has played an important role in individual identification and paternity testing, RNA technology is showing more and more wide application in prospect. This article reviews the application and progress of RNA in forensic science including estimation of postmortem interval, bloodstain age, wound age, as well as determination of cause of death and the source of body fluids.

A 472-SNP panel for pairwise kinship testing of second-degree relatives.

Kinship testing based on genetic markers, as forensic short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), has valuable practical applications. Paternity and first-degree relationship can be accurately identified by current commonly-used forensic STRs and reported SNP markers. However, second-degree and more distant relationships remain challenging. Although ∼105-106 SNPs can be used to estimate relatedness of higher degrees, genome-wide genotyping and analysis may be impractical for forensic use. With rapid growth of human genome data sets, it is worthwhile to explore additional markers, especially SNPs, for kinship analysis. Here, we reported an autosomal SNP panel consisted of 342 SNP selected from >84 million SNPs and 131 SNPs from previous systems. We genotyped these SNPs in 136 Chinese individuals by multiplex amplicon Massively Parallel Sequencing, and performed pairwise gender-independent kinship testing. The specificity and sensitivity of these SNPs to distinguish second-degree relatives and the unrelated was 99.9% and 100%, respectively, compared with 53.7% and 99.9% of 19 commonly-used forensic STRs. Moreover, the specificity increased to 100% by the combined use of these STRs and SNPs. The 472-SNP panel could also greatly facilitate the discrimination among different relationships. We estimated that the power of ∼6.45 SNPs were equivalent to one forensic STR in the scenario of 2nd-degree relative pedigree. Altogether, we proposed a panel of 472 SNP markers for kinship analysis, which could be important supplementary of current forensic STRs to solve the problem of second-degree relative testing.

[Polymorphisms analysis of mitochondrial DNA in coding area].

OBJECTIVE: To analyze mitochondrial DNA (mtDNA) polymorphisms in coding area and provide a theoretical basis for applying in forensic science. METHODS: The primers of 8162F/8483R and 13070F/13299R were designed according to the Anderson's sequence. Using PCR-sequencing method to detect polymorphisms of mtDNA nt8162-8483 and nt13070-13299. RESULTS: The lengths of the amplicons were 322 bp and 230 bp respectively. There were 24 mitochondrial haplotypes defined by 21 variable positions in both regions. The gene diversity was estimated at 0.751 1, and the probability of two randomly selected individuals having identical mtDNA types was 0.256 4. CONCLUSION: The polymorphic sites within mtDNA coding area can be useful in combination with mtDNA control region in order to increase the discrimination power.

Exploring the efficacy of paternity and kinship testing based on single nucleotide polymorphisms.

Short tandem repeats (STRs) are conventional genetic markers typically used for paternity and kinship testing. As supplementary markers of STRs, single nucleotide polymorphisms (SNPs) have less discrimination power but broader applicability to degraded samples. The rapid improvement of next-generation sequencing (NGS) and multiplex amplification technologies also make it possible now to simultaneously identify dozens or even hundreds of SNP loci in a single pool. However, few studies have been endeavored to kinship testing based on SNP loci. In this study, we genotyped 90 autosomal human identity SNP loci with NGS, and investigated their testing efficacies based on the likelihood ratio model in eight pedigree scenarios involving paternity, half/full-sibling, uncle/nephew, and first-cousin relationships. We found that these SNPs might be sufficient to discriminate paternity and full-sibling, but impractical for more distant relatives such as uncle and cousin. Furthermore, we conducted an in silico study to obtain the theoretical tendency of how testing efficacy varied with increasing number of SNP loci. For each testing battery in a given pedigree scenario, we obtained distributions of logarithmic likelihood ratio for both simulated relatives and unrelated controls. The proportion of the overlapping area between the two distributions was defined as a false testing level (FTL) to evaluate the testing efficacy. We estimated that 85, 127, 491, and 1,858 putative SNP loci were required to discriminate paternity, full-sibling, half-sibling/uncle-nephew, and first-cousin (FTL, 0.1%), respectively. To test a half-sibling or nephew, an additional uncle relative could be included to decrease the required number of putative SNP loci to ∼320 (FTL, 0.1%). As a systematic computation of paternity and kinship testing based only on SNPs, our results could be informative for further studies and applications on paternity and kinship testing using SNP loci.

Preparation of Pd-Co-based nanocatalysts and their superior applications in formic acid decomposition and methanol oxidation.

Formic acid (FA) and methanol, as convenient hydrogen-containing materials, are most widely used for fuel cells. However, using suitable and low-cost catalysts to further improve their energy performance still is a matter of great significance. Herein, PdCo and PdCo@Pd nanocatalysts (NCs) are successfully prepared by the facile method. Pd 3d binding energy decreases due to the presence of Co. Consequently, PdCo@Pd NCs exhibit high catalytic activity and selectivity toward FA dehydrogenation at room temperature. The gas-generation rate at 30 min is 65.4 L h(-1) g(-1) . PdCo/C has the worst catalytic performance in this reaction, despite the fact that it has a high gas-generation rate in the initial 30 min. Furthermore, both PdCo and PdCo@Pd NCs have enhanced electrocatalytic performance toward methanol oxidation. Their maximum currents are 966 and 1205 mA mg(-1) , respectively, which is much higher than monometallic Pd/C.