Analysis of Trio Half Sibling Testing / 法医学杂志

OBJECTIVES@#To establish an analytical method for half sibling testing involving common three relatives' participation.@*METHODS@#Based on the half sibling testing scenarios with the known biological mother, grandfather or uncle, and two unidentified controversial half siblings participating, two opposing hypotheses were set. Lineage reconstruction according to Mendel's law of heredity was carried out, and the calculation formula of the half sibling kinship index was derived. Verification of actual cases was carried out and the results were compared with duo half sibling testing.@*RESULTS@#In the scenarios of the known biological mother, grandfather and uncle participating in half sibling testing, the kinship calculation formulae of 54, 91 and 99 genotype combinations for kinship index calculation were deduced respectively. The actual cases showed higher kinship indexes in trio half sibling testing compared with duo half sibling testing.@*CONCLUSIONS@#It is beneficial to obtain more genetic information for family reconstruction and improvement of the strength of genetic evidence for half sibling testing by adding known relatives.

Evaluation of Detection Efficiency for Trio Full Sibling Testing / 法医学杂志

OBJECTIVES@#To study the detection efficiency of trio full sibling with another known full sibling reference added under different number of autosomal STR typing systems.@*METHODS@#Based on 43 detection systems consisting of 13 to 55 representative autosomal STR loci, 10 000 true families (full sibling group) and 10 000 false families (unrelated individual group) were randomly simulated. The full sibling index (FSI) was calculated based on the method of family reconstruction. The cumulative sibling relationship index (CFSI) of 0.000 1 and 10 000 were used as the evaluation thresholds, and the detection efficiency parameters were calculated and compared with the identification of the duo full sibling testing.@*RESULTS@#With the increasing number of STR loci, the error rate and inability of judgement rate gradually decreased; the sensitivity, specificity, correct rate of judgment and other parameters gradually increased, and the system efficiency gradually improved. Under the same detection system, trio full sibling testing showed higher sensitivity, specificity, system efficiency and lower inability of judgement rate compared with duo full sibling testing. When the system efficiency was higher than 0.85 and inability of judgement rate was less than 0.01%, at least 20 STRs should be detected for trio full sibling testing, which was less than 29 STRs required by duo full sibling testing.@*CONCLUSIONS@#The detection efficiency of trio full sibling testing is superior to that of duo full sibling testing with the same detection system, which is an effective identification scheme for laboratories with inadequate detection systems or for materials with limited conditions.

Research Progresses of Tri-Allelic Patterns in Autosomal STR in Forensic DNA Analysis / 法医学杂志

Tri-allelic pattern in autosomal STR is a common abnormal typing phenomenon in forensic DNA analysis, which brings difficulties and uncertainties to the evaluation of the evidence weight in actual cases. This paper reviews the types, formation mechanism, occurrence frequency, genetic pattern and quantitative evaluation of evidence of the tri-allelic pattern in autosomal STR in forensic DNA analysis. This paper mainly explains the formation mechanism and genetic patterns based on different types of tri-allelic pattern. This paper also discusses the determination of tri-allelic pattern and the quantitative method of evidence evaluation in paternity testing and individual identification. This paper aims to provide references for scientific and standardized analysis of this abnormal typing phenomenon in forensic DNA analysis.

Methods and Research Hotspots of Forensic Kinship Testing / 法医学杂志

Kinship testing is widely needed in forensic science practice. This paper reviews the definitions of common concepts, and summarizes the basic principles, advantages and disadvantages, and application scope of kinship analysis methods, including identity by state (IBS) method, likelihood ratio (LR) method, method of moment (MoM), and identity by descent (IBD) segment method. This paper also discusses the research hotspots of challenging kinship testing, complex kinship testing, forensic genetic genealogy analysis, and non-human biological samples.

Abdominal puncture drainage alleviates severe acute pancreatitis in rats by activating Nrf-2/HO-1 pathway and promoting autophagy / 南方医科大学学报

OBJECTIVE@#To assess the effect of early abdominal puncture drainage (APD) on autophagy and Nrf-2/HO-1 pathway in rats with severe acute pancreatitis (SAP) and explore the possibile mechanism.@*METHODS@#Thirty-two male SD rats were randomly divided into sham-operated (SO) group, SAP group with retrograde injection of 4% sodium taurocholate, APD group with insertion of a drainage tube into the lower right abdomen after SAP induction, and APD + ZnPP group with intraperitoneal injection of 30 mg/kg ZnPP 12 h before APD modeling. Blood samples were collected from the rats 12 h after modeling for analysis of amylase and lipase levels and serum inflammatory factors. The pathological changes of the pancreatic tissue were observed with HE staining. Oxidative stress in the pancreatic tissue was detected with colorimetry, and sub-organelle structure and autophagy in pancreatic acinar cells were observed by transmission electron microscopy. The expressions of autophagy-related proteins and Nrf-2/HO-1 pathway were detected using RT-PCR and Western blotting.@*RESULTS@#Compared with those in SAP group, the rats with APD treatment showed significantly alleviated pathologies in the pancreas, reduced serum levels of lipase, amylase and inflammatory factors, lowered levels of oxidative stress, and activated expressions of Nrf-2/HO-1 pathway in the pancreas. The ameliorating effect of ADP was significantly inhibited by ZnPP treatment before modeling. APD obviously reversed mitochondrial and endoplasmic reticulum damages and p62 accumulation induced by SAP.@*CONCLUSION@#APD treatment can suppress oxidative stress and repair impaired autophagy in rats with SAP by activating the Nrf-2/HO-1 pathway, thereby reducing the severity of SAP.

Role of CaMK II in pancreatic injury in mice with severe acute pancreatitis / 南方医科大学学报

OBJECTIVE@#To investigate the expression of Ca2+/calmodulin-dependent protein kinase II (CaMK Ⅱ) in pancreatic tissues of mice with severe acute pancreatitis (SAP) and explore the protective effect of KN93, a CaMK Ⅱ inhibitor, against pancreatic injury in SAP and the possible mechanism.@*METHODS@#Thirty-six healthy male C57 mice were randomly divided into sham operation group, SAP group, KN93 group and SAP + KN93 group (n=9). Serum and pancreatic tissue samples were collected 24 h after modeling. The pathological changes in the pancreatic tissues were observed using HE staining. Serum lipase and amylase activities and the levels of inflammatory factors were detected using ELISA. Western blotting was used to detect the expressions of CaMK Ⅱ, p-CaMK Ⅱ, p-NF-κB, MAPK and p-MAPK in mouse pancreas.@*RESULTS@#Compared with those in sham operation group, the expressions of p-CaMK Ⅱ, p-NF-κB and p-MAPK were significantly increased in SAP group (P < 0.05). KN93 treatment obviously alleviated pathological injuries of the pancreas in SAP mice, and significantly lowered serum levels of lipase, amylase and inflammatory factors (TNF-α and IL-6) and phosphorylation levels of NF-κB, ERK and MAPK proteins (P < 0.05).@*CONCLUSION@#The activity of CaMK Ⅱ is significantly increased in the pancreatic tissue of SAP mice. KN93 can alleviate pancreatic injury and inflammation in SAP mice possibly through the ERK/MAPK signaling pathway.

Preparation and evaluation of methotrexate sustained-release particles using crosslinked cyclodextrin metal-organic frameworks / 药学学报

Methotrexate (MTX) injection has a short half-life and significant toxic side effects. In order to overcome the demerits of MTX injection, MTX@COF was prepared for subcutaneous injection by loading MTX in crosslinked cyclodextrin metal-organic framework (COF) in this study. The cationic lipid material (2, 3-dioleoyl-propyl)-trimethylamine (DOTAP) was then coated on the MTX@COF surface by solvent evaporation. Different surface charge characteristics were observed in the coated MTX@COF@DOTAP with no significant change in particle morphology. The in vitro release behaviors of sustained-release particles were investigated in water and phosphate buffer (pH 7.4), and the in vivo release characteristics were evaluated for pharmacokinetics in rats. The in vitro release results showed that the cumulative release of MTX, MTX@COF and MTX@COF@DOTAP within 6 h was 92.70%, 36.31% and 18.19% in water, respectively; the cumulative release of MTX, MTX@COF and MTX@COF@DOTAP within 4 h was 90.82%, 79.37% and 58.30% in phosphate buffer, respectively; the results showed that MTX@COF can significantly delay the release of MTX, the modification to MTX@COF by DOTAP can further delay the release of MTX. Pharmacokinetic studies in rats showed that the mean retention time [MRT(0-t)] and the time to peak (Tmax) of the subcutaneous injection of MTX@COF@DOTAP group were significantly prolonged compared with the MTX@COF group and the MTX group. The area under the concentration-time curve [AUC(0-t)] of the MTX@COF@DOTAP subcutaneous injection group was 1.8 times high as that of the MTX group. In this study, MTX@COF@DOTAP particles had a certain sustained-release effect, and could prolong the bioavailability of MTX by subcutaneous injection, which provided a new idea for the development of new MTX dosage forms.

Formula Derivation for the Probability Distribution of IBS Score in Unrelated Individual Pairs / 法医学杂志

@#Objective To derive the general equation of the probability distribution of identity by state （IBS） score among biological full sibling pairs by calculating STR allele frequency. Methods Based on the Mendelian genetics law and the hypothesis that parents of biological full siblings（FS） were unrelated individuals, the IBS score and corresponding probability of different genotype combinations in the offspring when unrelated individuals of different genotype combinations give birth to two offsprings were derived. Results Given fi （i=1, 2, …, m） as the frequency of the ith allele of a STR locus, the probability of sharing 2 alleles（p2FS）, 1 allele（p1FS） or 0 allele （p0FS） with biological full sibling pairs on the locus can be respectively expressed as follows： p2FS= 14 ×[1 + 2∑im= 1 fi2 + 2（∑im= 1 fi2）2 -∑im= 1 fi4] , p1FS= 12 ×[1 +∑im= 1 fi2 - 2（∑im= 1 fi2）2 - 2∑im= 1 fi3 + 2∑im= 1 fi4] and p0FS= 14 ×[1 - 4∑im= 1 fi2 + 2（∑im= 1 fi2）2 + 4∑im= 1 fi3 -3∑im= 1 fi4] . The sum of p2FS, p1FS and p0FS must be 1. As for the multiple genotyping system that contained n STR loci, IBS scores between biological full sibling pairs conform to binomial distribution：IBS~B（2n, π1）. The population rate π1, can be given by the formula：π1= 1n∑ln= 1 p2FSl + 21n∑ln= 1 p1FSl . Conclusion The alternative hypothesis in biological full sibling testing is that two appraised individuals are biological full siblings. The probability of the corresponding alternative hypothesis of any STR locus combination or IBS score can be directly calculated by the equations presented in this study, and the calculation results are the basis for explanations of the evidence.

Equation Derivation of the Probability Distribution of IBS Score among Full Sibling Pairs / 法医学杂志

Objective To derive the general equation of the probability distribution of identity by state （IBS） score among biological full sibling pairs by calculating STR allele frequency. Methods Based on the Mendelian genetics law and the hypothesis that parents of biological full siblings （FS） were unrelated individuals, the IBS score and corresponding probability of different genotype combinations in the offspring when unrelated individuals of different genotype combinations give birth to two offsprings were derived. Results Given fi （i=1, 2, …, m） as the frequency of the ith allele of a STR locus, the probability of sharing 2 alleles （p2FS）, 1 allele （p1FS） or 0 allele （p0FS） with biological full sibling pairs on the locus can be respectively expressed as follows： (see the text). The sum of p2FS, p1FS and p0FS must be 1. As for the multiple genotyping system that contained n STR loci, IBS scores between biological full sibling pairs conform to binomial distribution： IBS~B（2n, π1）. The population rate π1, can be given by the formula： (see the text). Conclusion The alternative hypothesis in biological full sibling testing is that two appraised individuals are biological full siblings. The probability of the corresponding alternative hypothesis of any STR locus combination or IBS score can be directly calculated by the equations presented in this study, and the calculation results are the basis for explanations of the evidence.

Ancestry Inference Using the ForenSeqTM DNA Signature Prep Kit / 法医学杂志

Objective To evaluate the effect of 56 ancestry informative single nucleotide polymorphism （aiSNP） genetic markers in the ForenSeqTM DNA Signature Prep Kit on ancestry inference. Methods A total of 85 samples from five populations including Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population, Xinjiang Uygur autonomous region Uygur population and Nigerian population were collected. The library was constructed with the ForenSeqTM DNA Signature Prep Kit and sequencing was performed based on the MiSeq FGx Forensic Genomics System. Using universal analysis software （UAS） of ForenSeqTM, principal component analysis （PCA）, Structure and likelihood ratio method was used on the genotyping data of 56 aiSNP markers, respectively, and the genetic relationships between populations and inference of the origin of ancestors were analyzed. Results Among the five populations tested, the four ethnic populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population and Xinjiang Uygur autonomous region Uygur population） could be significantly distinguished from Nigerian population. Xinjiang Uygur autonomous region Uygur individuals were shown as having mixed origins of ancestors and could be distinguished from the other three Chinese populations. However, the other three populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population and Tibet autonomous region Tibetan population） could not be effectively distinguished by the system. Conclusion The 56 aiSNP markers in the ForenSeqTM DNA Signature Prep Kit can make accurate ancestry inference from the intercontinental level, but it is not yet able to distinguish between Chinese subpopulations.

Full Sibling Testing Based on NGS-SNP Genotyping Method and IBS Strategy / 法医学杂志

Objective To evaluate the effectiveness of single nucleotide polymorphism （SNP） genoty-ping in combination with identity by state （IBS） strategy in full sibling testing. Methods Thirty-five blood samples were collected from a four-generation family. Ninety autosomal SNPs were genotyped using Precision ID Identity Panel. The distribution of IBS scores for full siblings and other relationships were calculated and compared. The relationships were determined using Fisher discriminant function and threshold method, respectively. Results Based on family members and previous research, 44, 30, 111, 71 and 1 000 pairs of full siblings （FS）, grandparent-grandchild （GG）, uncle/aunt-nephew/niece （UN）, first cousins （FC） and unrelated individuals （UI） were obtained, respectively. The average IBS scores were 148, 130, 132, 124 and 120, respectively. Except for the GG and UN pairs, the distribution differences among the other relationships had statistical significance （P<0.05）. The false rates of Fisher discriminant function to determine relationships were 1.3%, 22.3%, 17.0% and 38.7% for FS, GG, UN and FC, respectively. Based on the simulation data, the thresholds t1=128 and t2=141 were recommended to determine full sibling relationships （the false rate ≤0.05%）. Conclusion The 90 SNP genetic markers included in the Precision ID Identity Panel meet the testing requirements for full sibling relationships. The threshold method based on IBS has a relatively lower false rate and is more flexible.

The immune response in acute and chronic pancreatitis / 解放军医学杂志

Acute and chronic pancreatitis are most common gastrointestinal diseases.Recently,there are emerging evidences that immune cell play important roles in the pathogenesis of acute and chronic pancreatitis.Studies have shown that macrophages,high mobility group protein 1 (HMGB 1) and interleukin-33 (IL-33) play an important role in the pathological process of pancreatitis,and are regulated by multiple levels.For example,immune cells are critical in the development and progression of pancreatitis,which not only have the ability to induce microenvironment,but also respond to danger signals derived from endogenous and exogenous molecules.Therefore,further understanding of relevant immune signaling will provide new idea and potential therapeutic targets that can prevent disease progression.Here,we review recent data from animal and human clinical studies that focus on immune responses.

Full Sibling Identification by IBS Scoring Method and Establishment of the Query Table of Its Critical Value / 法医学杂志

OBJECTIVES@#To establish a query table of IBS critical value and identification power for the detection systems with different numbers of STR loci under different false judgment standards.@*METHODS@#Samples of 267 pairs of full siblings and 360 pairs of unrelated individuals were collected and 19 autosomal STR loci were genotyped by Goldeneye™ 20A system. The full siblings were determined using IBS scoring method according to the 'Regulation for biological full sibling testing'. The critical values and identification power for the detection systems with different numbers of STR loci under different false judgment standards were calculated by theoretical methods.@*RESULTS@#According to the formal IBS scoring criteria, the identification power of full siblings and unrelated individuals was 0.764 0 and the rate of false judgment was 0. The results of theoretical calculation were consistent with that of sample observation. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci was successfully established.@*CONCLUSIONS@#The IBS scoring method defined by the regulation has high detection efficiency and low false judgment rate, which provides a relatively conservative result. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci provides an important reference data for the result judgment of full sibling testing and owns a considerable practical value.

Mutations in a Large Pedigree with Y-STR Genetic Markers / 法医学杂志

OBJECTIVE@#To explore the mutation of Y-STR loci in meiotic allelic transmission in a large pedigree.@*METHODS@#The oral swabs of 163 male individuals were collected from a Lin pedigree. Twenty-two Y-STR genetic markers were typed with AGCU Y24 fluorescent detection kit (AGCU Y24 system), which also contained 16 Y-STR markers included in Yfiler multiple amplification kit (Yfiler system). The genotyping results of Y-STR loci were compared between each two males in the pedigree.@*RESULTS@#There were 20 and 30 kinds of haplotypes obtained with Yfiler and AGCU Y24 systems in 163 male individuals from the Lin pedigree, respectively. The rates referred to haplotype differences (RRHD) of these two typing systems between male pairs were 0.910 5 and 0.922 7, respectively. The average number of marker differences were 6.582 1 and 9.824 8, respectively. The RRHD increased along with the incidents of meiosis.@*CONCLUSION@#Y-STR mutation leads to different Y-STR haplotypes among the male members in a paternal pedigree and the rate of difference increases along with the incidents of meiosis.

Expression Characteristics of KAI1 and Vascular Endothelial Growth Factor and Their Diagnostic Value for Hepatocellular Carcinoma

BACKGROUND/AIMS: We tried to investigate the expression characteristics of KAI1, a suppressor of wide-spectrum tumor metastasis, and vascular endothelial growth factor (VEGF), the most common angiogenesis factor, and then to analyze their diagnostic value for hepatocellular carcinoma (HCC). METHODS: The protein and mRNA expression levels of KAI1 or VEGF in HCC tissues and in self-controlled para-carcinoma tissues were analyzed by Western blot and real-time polymerase chain reaction, respectively. Serum levels of KAI1 and VEGF in the patients with HCC, benign liver disease or in healthy controls were quantitatively detected by enzyme-linked immunosorbent assay. RESULTS: The expression level of KAI1 was downregulated, while the expression level of VEGF was upregulated in the tissues or serum of the patients with HCC. The expression level of serum KAI1 in HCC patients was correlated with TNM staging, intrahepatic metastasis, lymph node or peritoneal metastasis, and portal vein thrombus. In addition to the factors that were correlated with KAI1 expression, VEGF expression was also closely related to the alpha-fetoprotein level of the patients. The area under the receiver operating characteristic curve for the diagnosis of HCC was 0.907 for KAI1 and 0.779 for VEGF. The sensitivity of serum KAI1 levels in the diagnosis of HCC was 86.96%; the accuracy was 83.06%, while the sensitivity, the accuracy and the negative predictive value were improved to 91.86%, 84.68%, and 78.79% according to the combined detection of KAI1 and VEGF, respectively. CONCLUSIONS: A combined detection of KAI1 and VEGF may greatly improve the efficiency of diagnosis and form a reliable panel of diagnostic markers for HCC.

Development of Chinese forensic Y-STR DNA database / 法医学杂志

Y chromosome is a male-specific paternal inherited chromosome. The STR markers on Y chromosome have been widely used in forensic practices. This article summarizes the characteristics of Y-STR and some factors are considered of selecting appropriate Y-STR markers for Chinese population. The prospects of existing and potential forensic applications of Y-STR profiles are discussed including familial excluding, familial searching, crowd source deducing, mixture sample testing, and kinship identifying. The research, development, verification of Y-STR kit, Y-STR mutation rate, and search software are explored and some suggestions are given.

Calculation of likelihood ratio for X-STR typing in kinship testing / 法医学杂志

OBJECTIVE@#To deduce the calculation formulae of likelihood ratio for kinship testing with X-short tandem repeat (X-STR) typing.@*METHODS@#With the identity by decent coefficient of different relationships, the joint genotypic probability of two individuals with specific genotypes was calculated as X value, and then the joint genotypic probability of two unrelated individuals was calculated as Y value; therefore, the likelihood ratio value (X/Y) was obtained.@*RESULTS@#The calculation formulae of the likelihood ratio for different genotype combinations of the female-female, female-male and male-male genetic relationships were derived and verified by real cases.@*CONCLUSION@#The calculation formulae are simple and accurate to evaluate the likelihood ratio for two individuals' genetic relationship with X-STR typing. The formulae provide the basic potential value for the difficult kinship testing with X-STR loci.

Mutation analysis for a Chinese family featuring X-linked alpha thalassemia/mental retardation syndrome / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To identify potential mutation in a Chinese family featuring X-linked alpha thalassemia/mental retardation syndrome (ATR-X).</p><p><b>METHODS</b>Based on clinical symptoms and inheritance pattern, linkage analysis of X chromosome short tandem repeats (X-STR) loci was carried out to locate the candidate gene. Subsequently, sequences of exons and exon-intron boundaries of the candidate gene were amplified with polymerase chain reaction (PCR). Potential mutations were detected by direct DNA sequencing. All patients were also analyzed for the trait of thalassemia.</p><p><b>RESULTS</b>Linkage analysis indicated the candidate gene to be ATRX. Subsequently, a homozygous missense mutation c.736C>T (p.R246C) was found in exon 9 of ATRX in all of the 3 patients. And a heterozygous mutation c.736C>T (p.R246C) was also identified in the patient's mother and grandmother. Similar mutations were not detected in other members of the family. Alpha thalassemia was detected in the proband and another patient, whose genotypes were determined as -α(3.7)/αα and --(sea)/αα, respectively.</p><p><b>CONCLUSION</b>Missense mutation of c.736C>T in ATRX gene is a mutation hotspot, and p.R246C may disturb the function of ATRX-DNMT3-DNMT3L domain (ADD), which may be responsible for the disease in this family.</p>

Analysis of allelic drop-out at short tandem repeat loci / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To explore the cause for allelic drop-out at short tandem repeat (STR) loci upon paternity testing with a PowerPlex® 16 kit.</p><p><b>METHODS</b>A total of 10 642 DNA confirmed paternity testing cases (18 314 parent/child allelic transfers) were analyzed with the PowerPlex® 16 kit. Samples suspected for having allelic drop-out were verified with an Identifiler™ kit and/or locus-specific singleplex amplification systems. PCR products of null alleles were separated and directly sequenced.</p><p><b>RESULTS</b>Eight cases of allelic drop-out were found. The overall rate of null allele in the PowerPlex® 16 system was 0.437 × 10(-3). DNA sequencing has confirmed single base variations within the binding region of published primers, in which 4 cases involved the D18S51 locus (2 cases with G>A transitions at 79 bp upstream of the repeats, 1 case with G>T transversion at 162 bp downstream of the repeats and 1 case with G>C transversion at 74 bp upstream of the repeats), 2 cases involved the D21S11 locus (1 case with C>A transversion at 17 bp upstream of the repeats and 1 case with A>G transition at 12 bp upstream of the repeats). One case involved the FGA locus (1 case with G>A transition at 142 bp downstream of the repeats) and 1 case involved TPOX locus (1 case with G>A transition at 198 bp downstream of the repeats).</p><p><b>CONCLUSION</b>Base variation in the primer binding region may cause failed PCR and result in null allele reports. Alternative primer sets should be used to verify the suspected allelic drop-out. Attention should be paid to this during paternity testing and data exchange for personal identification.</p>

Calculation of the avuncular index / 法医学杂志

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.