Due to the virtues of no stutter peaks, low rates of mutation, and short amplicon sizes, insertion/deletion (InDel) polymorphism is an indispensable tool for analyzing degraded DNA samples from crime scenes for human identifications (Wang et al., 2021). Herein, a self-developed panel of 43 InDel loci constructed previously by our group was utilized to evaluate the genetic diversities and explore the genetic background of the Han Chinese from Beijing (HCB) including 301 random healthy individuals. The lengths of amplicons at 43 InDel loci in this panel ranged from 87 to 199 bp, which indicated that the panel could be used as an effective tool to utilize highly degraded DNA samples for human identity testing. The loci in this panel were validated and performed well for forensic degraded DNA samples (Jin et al., 2021). The combined discrimination power (PD) and combined probability of exclusion (PE) values in this panel indicated that the 43 InDel loci could be used as the candidate markers in personal identification and parentage testing of HCB. In addition, population genetic relationships between the HCB and 26 reference populations from five continents based on 19 overlapped InDel loci were displayed by constructing a phylogenetic tree, principal component analysis (PCA), and population genetic structure analysis. The results illustrated that the HCB had closer genetic relationships with the Han populations from Chinese different regions.
Beijing ; China ; Forensic Genetics/methods* ; Gene Frequency ; Genetics, Population ; Humans ; INDEL Mutation ; Phylogeny

OBJECTIVES: To investigate the genetic polymorphism of InDel loci in SifalnDel 45plex system in the Han population in Jiangsu Province and the Mongolian population in Inner Mongolia, and to evaluate the effectiveness of the system in forensic medicine. METHODS: SifaInDel 45plex system was used for genotyping in blood samples of 398 unrelated individuals from the above two populations, and allele frequencies and population genetic parameters of the two populations were calculated respectively. Eight intercontinental populations in the gnomAD database were used as reference populations. The genetic distances between the two studied populations and eight reference populations were calculated based on the allele frequencies of 27 autosomal-InDels (A-InDels). The phylogenetic trees and multidimensional scaling (MDS) analysis diagrams were constructed accordingly. RESULTS: Among two studied populations, the 27 A-InDels and 16 X-InDels showed no linkage disequilibrium between each other and the allele frequency distributions were in Hardy-Weinberg equilibrium. The CDP of the 27 A-InDels in two studied populations were all higher than 0.999 999 999 9, and the CPE_trio were all less than 0.999 9. The CDP of the 16 X-InDels in Han in Jiangsu and Mongolian in Inner Mongolia female and male samples were 0.999 997 962, 0.999 998 389, and 0.999 818 940, 0.999 856 063, respectively. The CMEC_trio were all less than 0.999 9. The results of population genetics showed that the Jiangsu Han nationality, Inner Mongolia Mongolian nationality and East Asian population clustered into one branch, showing closer genetic relationship. The other 7 intercontinental populations clustered into another group. And the above 3 populations displayed distant genetic relationships with the other 7 intercontinental populations. CONCLUSIONS The InDels in the SifaInDel 45plex system have good genetic polymorphism in the two studied populations, which can be used for forensic individual identification or as an effective complement for paternity identification, and to distinguish different intercontinental populations.
Humans ; Phylogeny ; Gene Frequency ; Polymorphism, Genetic ; Genetics, Population ; Asian People/genetics* ; China ; INDEL Mutation

Genetic markers in forensic DNA typing experienced the variable number of tandem repeats （VNTR） sequences and the short tandem repeats （STR） sequences. With the emerge of sequencing technology, the third generation of genetic markers were found out, which usually have two alleles including single nucleotide polymorphism （SNP） and insertion/deletion （InDel）, also known as biallelic genetic markers. Because of the insertions or deletions of DNA fragments, InDel genetic marker reveals DNA fragment length polymorphism and widely distributes across the whole genome. InDel genetic marker is numerous and has the characteristics of STR and SNP genetic markers, which has been applied in the fields of genetics and anthropology. This review focuses on the research progress of InDel genetic marker in forensic science, aiming to review and summarize the main research findings in recent years and provide clues for future researches.
Alleles ; DNA/genetics* ; DNA Fingerprinting ; Forensic Genetics ; Genetic Markers ; INDEL Mutation ; Microsatellite Repeats ; Polymorphism, Single Nucleotide

Objective To explore the genetic background and structure of Urumqi Mongolians, the previously developed 39-AIM-InDels panel for ancestry inference was utilized in the present study. Methods The blood samples of 145 unrelated healthy Urumqi Mongolian individuals were collected and genotyped. The compositions of ancestry information of Urumqi Mongolians were studied with 17 different populations from three continents （East Asia, Europe and Africa） as reference populations. Then, multiple population genetics and bioinformatics analysis methods were applied, the Fst and DA values between matched populations were compared and analyzed, PCA analysis was performed and a phylogenetic tree was constructed. The proportions of ancestry information components of Urumqi Mongolians were analyzed with Structure software, etc. Results The ancestry information components of Urumqi Mongolian group in different intercontinental populations accounted for 89%, 7%, and 3% of East Asian, European, and African populations, respectively. Compared with other intercontinental populations, Urumqi Mongolian group and East Asian populations have lower Fst and DA values, and they were in the same cluster in PCA analysis as well. In a phylogenetic tree, the Urumqi Mongolian group was in the same branch as East Asian populations. Conclusion Urumqi Mongolian group had relatively close genetic relationships with East Asian populations, and the proportion of its East Asian ancestry was about 89%.
Asian People/genetics* ; Forensic Genetics ; Gene Frequency ; Genetics, Population ; Humans ; INDEL Mutation ; Phylogeny ; Polymorphism, Single Nucleotide

OBJECTIVETo identify some closely related Lycoris species and evaluate interspecific relationships among them.

METHODThe cpDNA trnL-F sequence of 20 taxa representing 15 species of Lycoris and Narcissus tazaetta var. chinensis as one out-group were determined by using direct sequencing of PCR product, and they were analyzed by means of the software of CLUSTRAL and MEGA.

RESULTThe length of trnL-F of all taxa was 905 - 1 036 bp. When the gaps were always treated as missing, there were 14 variable sites and 10 parsim-info sites, which could be used to identify some species of Lycoris. Four nucleotides inserteions/deletions were significant different among Lycoris and two species of Narcissus. Phylogeny tree was constructed with the maximum parsimony methods by bootstrap test. Three infrageneric clades of all Lycoris species were resolved. The classification was basically consistent with that of morphology except for L. longituba, L. aurea, and L. straminea.

CONCLUSIONThe tree suggested that L. anhuiensis can not be taken as an independent species, while it may be of a variety or a hybrid of L. longituba. Regarding the hybrid origin species, the materal parent of L. rosea and L. haywardii was revealed to be L. sprengeri. There were some variations in the trnL-F sequence, which were good molecular markers for identification species of Lycoris.

Cluster Analysis ; Drugs, Chinese Herbal ; Genes, Plant ; genetics ; INDEL Mutation ; Lycoris ; classification ; genetics ; Mutation ; Nucleotides ; genetics ; Phylogeny ; Sequence Analysis, DNA

OBJECTIVES: The previously established 38-plex InDel system was optimized and its performance was validated according to the Scientific Working Group on DNA Analysis Method (SWGDAM) application guidelines. The ancestry inference accuracy of individuals from East Asian, European, African and mixed populations was verified. METHODS: DNA standard sample 9947A was used as the template to establish the optimal amplification conditions by adjusting primer balance, Mg²⁺ final concentration and optimizing PCR thermal cycle parameters and amplification volume. The allelic dropout, nonspecific amplification and whether the origin of the inferred samples matched the known information were compared to evaluate the performance of this system. RESULTS: The optimal dosage of this system was 0.125-2 ng DNA template. The results of InDel typing were accurate, the amplification equilibrium was good, and the species specificity was good. This system showed certain tolerance to DNA samples including the inhibitor such as hemoglobin (≤80 μmol/L), indigo (≤40 mmol/L), calcium ion (≤1.0 mmol/L), and humic acid (≤90 ng/μL). The system enabled the direct amplification of DNA from saliva and blood on filter paper, and the results of ethnic inference were accurate. The system successfully detected the mixed DNA sample from two individuals. The test results of the system for common biological materials in practical cases were accurate. CONCLUSIONS The results of the 38-plex InDel system are accurate and reliable, and the performance of the system meets the requirement of the SWGDAM guidelines. This system can accurately differentiate the ancestry origins of individuals from African, European, East Asian, and Eurasian populations and can be implemented in forensic practice.
Humans ; Polymorphism, Single Nucleotide ; Genotype ; Polymerase Chain Reaction ; DNA/genetics* ; DNA Fingerprinting/methods* ; INDEL Mutation ; Genetics, Population ; Gene Frequency

OBJECTIVES: To investigate the genetic information of 57 autosomal InDel loci (A-InDels) included in AGCU InDel 60 fluorescence detection kit in the Beichuan Qiang population of Sichuan Province and evaluate its application value in forensic medicine. METHODS: A total of 200 unrelated healthy individuals from Beichuan Qiang population of Sichuan Province were typing detected by AGCU InDel 60 fluorescence detection kit. Allele frequencies and population genetic parameters of the 57 A-InDels were statistically analyzed and compared with the available data of 26 populations. RESULTS: After Bonferroni correction, there was no linkage disequilibrium between the 57 A-InDels, and all loci were in Hardy-Weinberg equilibrium. Except for rs66595817 and rs72085595, the minor allele frequencies of 55 A-InDels were above 0.3. PIC ranged from 0.298 3 to 0.375 0, CDP was 1-2.974 8×10^-24, CPE_duo was 0.999 062 660, and CPE_trio was 0.999 999 999. The calculation of the genetic distance showed that Beichuan Qiang population had the closest genetic distances with Beijing Han and South China Han populations, but far away from African populations. CONCLUSIONS The 57 A-InDels in AGCU InDel 60 fluorescence detection kit have a good genetic polymorphism in Beichuan Qiang population of Sichuan Province, which can be used as effective supplemental for individual identification and paternity identification in forensic medicine.
Humans ; Genetics, Population ; Asian People/genetics* ; Polymorphism, Genetic ; Gene Frequency ; INDEL Mutation ; China ; Microsatellite Repeats ; Genetic Loci

The molecular markers(cpSSR, cpSNP and cpIndel) were developed based on the whole genome sequence of Panax notoginseng chloroplast genome, which provide a powerful tool for the evaluation and analysis of the future P. notoginseng germplasm resources. The 89 P. notoginseng samples from 9 groups were used for the experiment, and the data for the study were derived from NCBI and the GenBank numbers were: KJ566590, KP036468, KR021381 and KT001509. Through sequence alignment, 30 polymorphic sites(SNP and Indel) were identified, including 16 cpSNP and 14 cpIndel; cpSNP and cpIndel accounted for far more than the gene region in the intergenic region. The developed cpSSR reached 87-89, the repeat unit was mainly composed of trinucleotide, accounting for 70%-71%, and the dinucleotide was the least, accounting for 7%. Eighteen cpDNA molecular markers were developed, including 7 cpSSR primers, 6 cpIndel primers, and 5 cpSNP primers. The MatK gene and ycf1 primers were chosen as control. According to the results of DNA gel electrophoresis, cpSSR-5, pgcpir019 and pncp08 can be used to distinguish different cultivated populations of P. notoginseng. Among them, cpSSR-5 and pgcpir019 can also be used to distinguish the inter-species resources of ginseng by comprehensive sequence length, population π value and average nucleotide difference. However, pncp08 can only be used to distinguish different populations of P. notoginseng. In addition, the effect of distinguishing the groups of P. notoginseng, which the primer pncp-M(based on the MatK gene) is weaker than the cpSSR-5, pgcpir019 and pncp08.
DNA, Chloroplast/genetics* ; Genetic Markers ; Genetics, Population ; INDEL Mutation ; Panax notoginseng/genetics* ; Polymorphism, Single Nucleotide ; Sequence Alignment

OBJECTIVETo understand the influence of angiotensin converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism and beta3-adrenergic receptor (beta3-AR) gene Trp64Arg polymorphism on fetal growth and neonatal insulin sensitivity.

METHODSTotally 296 newborn infants were selected into our study and divided into 2 groups according to gestational age and birth weight: adequate-for-gestational-age (AGA) group (222 cases) and small-for-gestational-age (SGA) group (74 case). Serum glucose and insulin were examined in the morning of the 3rd day before milk. Insulin sensitivity was evaluated by homeostasis model assessment (HOMA) equation. beta3-AR gene Trp64Arg polymorphism and ACE gene I/D polymorphism (202 cases) were analysed using polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) technique. Gestational age, birth weight, birth weight percentage, serum glucose, insulin and HOMA-IR were compared among different genotype groups. Statistical analysis was performed with the SPSS 10.0 software.

RESULTSNo significant difference was found between the serum glucose level of SGA group (4.03 +/- 1.05 mmol/L) and AGA group (4.05 +/- 1.14 mmol/L), P = 0.008. The serum insulin level (converted into Ln) of SGA group (2.262 +/- 0.746) was significantly higher than that of AGA group (1.757 +/- 0.805), P < 0.001. The HOMA-IR (also converted into Ln) level of SGA group (0.217 +/- 0.367) was also significantly higher than that of AGA group (0.001 +/- 0.378), P < 0.001. In the SGA group beta3-AR gene Arg64 allele carriers had higher serum insulin and HOMA-IR level (both changed to Ln, 2.654 +/- 0.701, 0.371 +/- 0.338) compared with noncarriers (2.074 +/- 0.698, 0.143 +/- 0.360), P < 0.05. The ACE gene DD genotype carriers had higher serum insulin and HOMA-IR level (both were converted into Ln, 2.19 +/- 0.91, 0.51 +/- 1.01) compared with II (1.77 +/- 0.85, 0.02 +/- 0.93) and ID genotype group (1.77 +/- 0.83, 0.05 +/- 0.91), P < 0.05. The ACE gene DD carriers had lower birth weight percentage compared with II and ID genotype group, P < 0.05. When both genes' polymorphisms were taken into account, the newborns who had both DD genotype and Arg64 allele had obviously higher serum insulin level (Ln, 2.560 +/- 1.160) than the neonates who had only one of the polymorphisms mentioned above (1.970 +/- 0.821, 1.992 +/- 0.706) and the neonates who had neither of the two polymorphisms (1.683 +/- 0.832), P < 0.05. The newborns who had both DD genotype and Arg64 allele also had significantly higher HOMA-IR level (Ln, 1.042 +/- 1.315) than the neonates who had only one of the polymorphisms mentioned above (0.247 +/- 0.710, 0.230 +/- 0.890) and the neonates who had neither of the two polymorphisms (-0.053 +/- 0.924), P < 0.05.

CONCLUSIONNewborns SGA had impaired insulin sensitivity. beta3-AR gene Trp64Arg polymorphism and ACE gene I/D polymorphism are important factors that may connect IUGR with insulin resistance syndrome in adulthood.

Female ; Fetal Development ; genetics ; Humans ; INDEL Mutation ; Infant, Newborn ; Infant, Small for Gestational Age ; Insulin Resistance ; Male ; Peptidyl-Dipeptidase A ; genetics ; Polymorphism, Genetic ; Receptors, Adrenergic, beta-3 ; genetics

OBJECTIVETo investigate whether the insertion/deletion(I/D) polymorphism in the angiotensin converting enzyme(ACE) gene is associated with essential hypertension in Xinjiang Kazakh isolated population.

METHODSThe study covered 201 hypertensives and 151 normotensive controls in Xinjiang Barlikun Kazakh population. The I/D polymorphism of ACE gene was determined by polymerase chain reaction.

RESULTSThe frequencies of D and I in the hypertensive group (0.44 and 0.56, respectively) were not significantly different from the controls(0.39 and 0.61, respectively, P=0.16). The frequencies of ACE genotypes of DD, ID, and II were 0.18, 0.52, 0.30 in hypertensives respectively and 0.17, 0.43, 0.40 in control group respectively. There was no significant difference in genotypes between hypertensive group and normotensive group (P=0.14).

CONCLUSIONThe results suggested that the I/D polymorphism of ACE gene might not be associated with hypertension in the Kazakh population of Xinjiang Barlikun area.

Asian Continental Ancestry Group ; genetics ; Blood Pressure ; genetics ; China ; ethnology ; Female ; Gene Frequency ; Humans ; Hypertension ; genetics ; INDEL Mutation ; Male ; Middle Aged ; Peptidyl-Dipeptidase A ; genetics ; Polymorphism, Genetic ; Population Groups