Autosomal InDel Research Articles

Population genetics of 30 insertion-deletion polymorphism in polish Populations

The Investigator DIPplex® kit (Qiagen) contains components for the simultaneous amplification and analysis of 30 biallelic autosomal InDels and amelogenin. The objective of this study was to estimate the diversity of the 30 markers in a Polish population sample (N = 389) and to evaluate their usefulness in forensic genetics. The DIPplex genotype distributions showed no significant deviation from Hardy-Weinberg rule expectations (Bonferroni corrected). The mean observed heterozygosity value is 0.4611, and the combined Matching Probability value is 1.08x10−13. The investigated marker set has been confirmed as a potential extension to standard STR - based kits or a separate informative system for individual identification and kinship analysis.

Genetic polymorphism of 30 autosomal InDel loci in Chinese Hainan Li population

A novel genetic marker, Insertion/Deletion polymorphism (InDel) shows remarkable potential for forensic DNA applications. Hainan Island is the southernmost and the second largest island in China, of which the Li ethnic group is regarded as the original inhabitants. In this study, 207 individual samples of Li ethnic group from Hainan were genotyped using Investigator DIPplex kit which contains 30 autosomal InDels and Amelogenin. Allele frequency and forensic parameters were calculated for these loci. Several deviations from Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) may indicate founder effect in the Li ethnic group. The combined power of discrimination (CPD) and the cumulative probability of exclusion (CPE) reached 0.99999999992912 and 0.9861, respectively. These results suggested that the kit was effective for personal identification in Hainan Li population. The population comparisons through the Nei’s standard genetic distance (Rst), phylogenetic tree, multidimensional scaling analysis (MDS), principal component analysis (PCA), and STRUCTURE analyses along continental divisions manifested that the 30 InDels panel had a certain intercontinental differentiation ability.

Development and validation of a multiplex insertion/deletion marker panel, SifaInDel 45plex system

In addition to commonly used short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because they combine desirable characteristics of both STRs and SNPs. In the present study, the SifaInDel 45plex system was designed to amplify 45 InDel markers, including 27 autosomal InDels (A-InDels), 16 X chromosome InDels (X-InDels) and two Y chromosome InDels (Y-InDels), simultaneously in a single PCR procedure and then detect products by capillary electrophoresis (CE). We also optimized the PCR conditions for the novel panel and performed several validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics.The results confirmed that full profiles could be obtained from ≥62.5 pg of input DNA and from a series of challenging samples encountered in routine casework. The SifaInDel 45plex panel could tolerate different concentrations of inhibitors, such as ≤50 μM hematin, ≤20 ng/μL nigrosine and ≤8000 ng/μL urea. In a population investigation, for the 27 A-InDels, the combined power of discrimination (CPD) exceeded 0.999999, and the combined power of exclusion in duos (CPED) and trios (CPET) was 0.955118 and 0.997754, respectively. For the 16 X-InDels, the combined PDMale and PDFemale was computed as 0.999845 and 0.999998, respectively, and the combined mean exclusion chance in father/daughter or mother/son duos (MECDuo) and mean exclusion chance in standard trios involving daughters (MECTrio) was 0.976220 and 0.998163, respectively. In addition, the two Y-InDels could play a role in correctly determining gender. Overall, the established SifaInDel 45plex panel is a well-performing, reliable and robust multiplex system that stands out for combining a considerable number of A-indels, X-indels and Y-indels based on a CE platform. The population study results also demonstrated that the SifaInDel 45plex panel could be a valid complementary approach for human identification and complex kinship analysis.

RETRACTED ARTICLE: Genetic analysis and forensic evaluation of 47 autosomal InDel markers in four different Chinese populations.

This study aims to investigate the population-wide genetic data and forensic efficiency of 47 autosomal InDels in the four Chinese populations of Chinese Han, Tibetan, Uighur, and Chinese Hui. The allele frequencies and forensic parameters of the 47 InDels were investigated in 638 unrelated individuals from these four populations. The results can serve as a reference database that includes InDels in the populations, and they can contribute to population diversity studies.

Developmental validation of a novel six-dye typing system with 47 A-InDels and 2 Y-InDels

In this study, a multiplex amplification system including 47 autosomal InDels, 2 Y-chromosome InDels, and the sex-determining marker (Amelogenin) was developed with six fluorescent dyes labeling. These InDels were selected from the previous study based on a series of criteria (0.3 < MAF < 0.5, HET > 0.4, etc). The system was designated the AGCU InDel 50 kit and was validated in a series of studies, including a degradation study; tests for sensitivity, species specificity, reproducibility, stability, applicability to case samples, balance of peak height, and PCR conditions; and a population study. The results showed that AGCU InDel 50 kit was quite sensitive, specific, stable in several PCR conditions or exposure to PCR inhibitors, especially against degradation. 74 case samples and 50 paternity cases with STR mutation events were tested using PowerPlex® 21 System, AGCU InDel 50 kit, and Investigator DIPplex kit, and the results showed that the ratio of loci detected with the developed kit were close to Investigator@ DIPplex kit, but considerably higher than PowerPlex® 21 System for case samples containing low amounts of degraded DNA. As for 50 paternity cases, no mutation was observed in any InDels locus, and the CPIs based on 47 autosomal InDels contained in the AGCU InDel 50 kit were all higher than those based on 30 InDels contained in Investigator® DIPplex kit, except 3 cases. In the population study, 203 unrelated individuals from the Guangdong Han population were detected using the AGCU InDel 50 kit, and the values of combined power of discrimination and combined power of exclusion were 0.999 999 999 999 999 and 0.9997, respectively. Thus, AGCU InDel 50 kit is suitable for individual identification and as a supplemental tool for paternity testing. It is reproducible, accurate and robust for forensic applications and human genetic studies.

Genetic structure and forensic parameters of 30 InDels for human identification purposes in 10 Tibetan populations of China

Insertion/deletion analysis can serve as a promising and useful supporting tool in forensic research. The Qiagen Investigator® DIPplex Kit contained 30 well-chosen autosomal InDels was targeted to reveal the population genetic variation. In the present study, 10 Tibetan populations residing in different geographic areas of China were recruited and genotyped by Investigator® DIPplex Kit. Allele frequencies and forensic parameters were determined. No significant departures from Hard-Weinberg equilibrium (HWE) in all loci/populations after Bonferroni correction. The combined matching probability values range from 1.7148 × 10−11 to 5.3516 × 10-1° in 10 Tibetan populations. Our results revealed 10 Tibetan populations in China are genetically very similar. Intercontinental population differentiation analysis indicated Tibetan populations had a close genetic relationship with East Asian populations using Hierarchical clustering, multi-dimensional scaling (MDS), principal component analysis (PCA) and STRUCTURE. Comprehensive population genetic studies revealed that the 30-InDels assay was similarly efficient in forensic personal identification and could be regarded as an effective supplementary protocol for kinship testing.

Evaluation of Population Data and Forensic Parameters of Turkish Population on 30 Autosomal Insertion and Deletion Polymorphisms

The InDel, based on the insertion or deletion in the human genome, is an alternative genetic marker for the widely used forensic STRs identification method. In this study we aim to determine forensic parameters of autosomal 30 InDel loci in Turkish population and to analyze the genetic differences between Turkish population and previously published other population data of alleged loci. We collected 250 blood samples from non-relative healthy volunteers. Then 30 insertion-deletion loci and amelogenin were amplified according to Investigator DIPplex® Kit manual (Qiagen). The PCR products were separated and analyzed. Forensic and population parameters of the 30 InDels were estimated with Promega PowerStats Excel worksheet, p-values of Hardy–Weinberg Equilibrium and FST test of population differentiation were calculated with Arlequin ver. 3.5. After Bonferonni correction the DIPplex allele frequency distributions showed no significant deviation from HWE. FST indicated that significant statistical differences were found between our population and Korean population at 16, Somalian population at 16, Taiwanian population at 9, Finnish population at 5, Polish population at 1 InDel loci. There is no statistically significant results in between our Turkish population sample, Turkish population in Denmark, and Italian populations in North-East Italy. We present population data and forensic parameters for 30 autosomal InDels studied in Turkish population samples. This data set will be useful in paternity, kinship analysis and also in identification of the forensic case samples. We also emphesis that Turkish population data is genetically closer to the nearby European populations as expected.

Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed.

In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate, and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8550 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96 × 10-11 and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the DA distance and Fst values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group, and several Han populations.

Genetic Polymorphism of 30 InDel Loci in Han Population from Jiangsu Province

To investigate the genetic information of 30 insertion/deletion （InDel） loci in Han population from Jiangsu Province, and to explore the application values of Investigator® DIPplex kit for guiding the forensic analysis in Han population from Jiangsu Province. The autosomal InDel loci of 305 unrelated healthy Han individuals from Jiangsu Province were genotyped and analysed by Investigator® DIPplex kit, and the allelic frequencies and forensic parameters of 30 InDel loci were statistically analysed. The distribution of 30 InDel loci in Han population from Jiangsu Province conformed to Hardy-Weinberg equilibrium. The minor allele frequencies of 21 InDel loci were above 0.3. The polymorphism information content ranged from 0.089 to 0.375, while the discrimination power distributed from 0.093 to 0.500. The paternity exclusion in duo cases and trio cases were 0.047-0.250 and 0.046-0.219, respectively. The linkage disequilibrium analysis of 30 InDel loci showed that all loci were independent from each other. The combined discrimination power was 1-7.369×10⁻⁸, whereas the combined mean exclusion chance in duo cases was 0.998 933 978, in trio cases was 0.997 806 392. The Fst values were all less than 0.06 except HLD118 and other four loci, which showed small differences between groups. The InDel loci of Investigator® DIPplex kit can be used as complementary genetic markers for the cases associated with forensic genetics.

A GHEP-ISFG collaborative study on the genetic variation of 38 autosomal indels for human identification in different continental populations

A collaborative effort was carried out by the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) to promote knowledge exchange between associate laboratories interested in the implementation of indel-based methodologies and build allele frequency databases of 38 indels for forensic applications. These databases include populations from different countries that are relevant for identification and kinship investigations undertaken by the participating laboratories. Before compiling population data, participants were asked to type the 38 indels in blind samples from annual GHEP-ISFG proficiency tests, using an amplification protocol previously described. Only laboratories that reported correct results contributed with population data to this study. A total of 5839 samples were genotyped from 45 different populations from Africa, America, East Asia, Europe and Middle East. Population differentiation analysis showed significant differences between most populations studied from Africa and America, as well as between two Asian populations from China and East Timor. Low FST values were detected among most European populations. Overall diversities and parameters of forensic efficiency were high in populations from all continents.

Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group.

In the present study, we assessed the genetic diversities of the Chinese Kazak ethnic group on the basis of 30 well-chosen autosomal insertion and deletion loci and explored the genetic relationships between Kazak and 23 reference groups. We detected the level of the expected heterozygosity ranging from 0.3605 at HLD39 locus to 0.5000 at HLD136 locus and the observed heterozygosity ranging from 0.3548 at HLD39 locus to 0.5283 at HLD136 locus. The combined power of discrimination and the combined power of exclusion for all 30 loci in the studied Kazak group were 0.999999999999128 and 0.9945, respectively. The dataset generated in this study indicated the panel of 30 InDels was highly efficient in forensic individual identifcation but may not have enough power in paternity cases. The results of the interpopulation differentiations, PCA plots, phylogenetic trees and STRUCTURE analyses showed a close genetic affiliation between the Kazak and Uigur group.

Population genetic data of 38 insertion-deletion markers in six populations of the northern fringe of the Iberian Peninsula

Insertion-deletions have been reported very useful markers for forensic purposes. To further deepen in this matter, 38 non-coding bi-allelic autosomal indels were analyzed in 575 individuals representing six populations from the northern fringe of the Iberian Peninsula. Autochthonous populations from the Basque Country, northern Navarre, the Pas Valley in Cantabria and Aragon were analyzed, together with non-autochthonous populations from the Basque Country and northern Navarre. At the intra-population level, all loci analyzed were in Hardy-Weinberg equilibrium except for marker rs33917182 in autochthonous Basques. Linkage disequilibrium (LD) test did not reveal statistically significant allelic association between the different loci pairs in all six populations. Forensic parameters proved to be highly informative in the six populations analyzed, even if a scenario with population substructure and local inbreeding was considered for match probability calculations, and the potential of this indels set to be used in combination with other genetic markers is remarkable. As for inter-population analyses, in general terms the six populations showed low but statistically significant genetic distances. However, though this indels set efficiently differentiate between main ancestries, it does not allow an accurate separation at a local level and, for the time being, their combination with other informative markers is needed to maximize the power to accurately differentiate populations with close genetic ancestry.

Genetic diversity of 38 insertion–deletion polymorphisms in Jewish populations

Population genetic data of 38 non-coding biallelic autosomal indels are reported for 466 individuals, representing six populations with Jewish ancestry (Ashkenazim, Mizrahim, Sephardim, North African, Chuetas and Bragança crypto-Jews). Intra-population diversity and forensic parameters values showed that this set of indels was highly informative for forensic applications in the Jewish populations studied. Genetic distance analysis demonstrated that this set of markers efficiently separates populations from different continents, but does not seem effective for molecular anthropology studies in Mediterranean region. Finally, it is important to highlight that although the genetic distances between Jewish populations were small, significant differences were observed for Chuetas and Bragança Jews, and therefore, specific databases must be used for these populations.

Autosomal indels distribution in Metropolitan Manila, Philippines

The Philippines are a group of islands in the Asia-Pacific region harboring a high diversity of cultures, languages and people due to various migration waves and different degrees of admixture between neighboring groups. In this work we studied the most populous region of the country – Metropolitan Manila – with a set of small autosomal insertion deletion (indel) polymorphisms, to assess their genetic diversity and usefulness in forensic context. Using a single-tube multiplex reaction we characterized 38 indels in 195 individuals born in the National Capital Region, allowing to establish an allele frequency database for future reference in forensic applications. The genetic diversity observed was high (average heterozygosity=0.40890), similar to previous studies in other East Asian populations, and the marker set reached good levels of informativeness, with a combined power of discrimination of 99.999999999997% and combined power of exclusion of 99.50%. In conclusion, our study showed that this simple indel multiplex can be useful for forensic applications in Metropolitan Manila Filipino population.

Genotyping of 38 insertion/deletion polymorphisms for human identification using universal fluorescent PCR

Short insertion/deletion (Indel) polymorphisms of approximately 2–6 bp are useful as biallelic markers for forensic analysis, and the application of Indel genotyping as a supplementary tool would improve human identification accuracy. We examined the allele frequencies of 37 autosomal Indels in the Japanese population and developed a novel dual-color genotyping method for human identification on the basis of universal fluorescent PCR, including the sex-typing amelogenin locus. Target genomic fragment sizes for 38 Indels were 49–143 bp. We analyzed these Indels in 100 Japanese individuals using the M13(-47) sequence as a universal primer. For dual-color genotyping, we designed a novel universal primer with high amplification efficiency and specificity. Using FAM-labeled M13(-47) and HEX-labeled modified M13(-47) primers, fluorescent signals at all loci were clearly distinguished in two independent multiplex PCRs. Average minor allele frequency was 0.39, and accumulated matching probability was 2.12 × 10−15. Complete profiles were successfully amplified with as little as 0.25 ng of DNA. This method provides robust, sensitive, and cost-effective genotyping for human identification.

Population genetics of 30 INDELs in populations of Poland and Taiwan

The Investigator DIPplex® kit (Qiagen) contain components for the simultaneous amplification and analysis of 30 biallelic autosomal INDELs and amelogenin. The objective of this study was to estimate the diversity of the 30 markers in Polish (N P = 122) and Taiwanese (N T = 126) population samples and to evaluate their usefulness in forensic genetics. All amplicon lengths were shorter than 160 base pairs. The DIPplex genotype distributions showed no significant deviation from Hardy–Weinberg rule expectations (Bonferroni corrected) except for DLH39 in the Taiwanese population. Among the Poles and the Taiwanese the mean observed heterozygosity values are 0.4385 and 0.4079, and the combined matching probability values are 7.98 × 10−14 and 1.22 × 10−11, respectively. The investigated marker set has been confirmed as a potential extension to standard short tandem repeat-based kits or a separate informative system for individual identification and kinship analysis. Eight INDELs have been selected as possible ancestry informative single-nucleotide polymorphisms for further analyses.

Genetic population data of 38 autosomal InDels for the Amerindian community Embera-Chami of Lapo, Antioquia-Colombia

This paper presents the genetic characterization of the Embera-Chami Amerindian community of Lapo-Antioquia-Colombia using 38 autosomal Indels. This group of markers showed a high discriminatory power (>99.9999%) and an appropriate power of exclusion (99.40%), allowing the use of these markers in the field of forensic genetics in this population.

Population genetic data of 38 autosomal InDels in San Basilio de Palenque, the first free town in America

In order to increase the information about Indels, we report allele frequencies and statistical parameters of forensic efficiency obtained typing a sample of 114 unrelated healthy individuals living in San Basilio de Palenque – Colombia using a panel of 38 autosomal InDels. No significant deviations from Hardy–Weinberg expectations were found except in the marker rs10629077 (p=0.0002). The present database will be useful for forensic and paternity purposes for the region studied. Moreover, these additional markers can help forensic laboratories to solve parentage testing as well as to improve the analysis of degraded DNA samples.

Population genetic data of 30 autosomal indels in Central Spain and the Basque Country populations

Samples from 71 unrelated Central Spain individuals and 60 Basque Country autochthonous individuals were typed with the Investigator DIPplex kit (30 biallelic autosomal mini-indels and amelogenin) and their allele frequencies were determined. Results demonstrated the assumption of independence within and between the loci analyzed. Different partially silent alleles were observed for the locus HLD97 (rs17238892) produced by a neighboring SNP (A/G), located 61 bp downstream from the main indel site as shown by sequencing analysis.

Comparative evaluation of alternative batteries of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs

Kinship investigations such as paternity are currently solved using sets of (commercially available) highly polymorphic autosomal short tandem repeats (STRs), which lead to powerful likelihood ratios (LR). Still, some difficult cases arise whenever the kinship is much more remote or if the alternative hypotheses are not correctly formulated due to the lack of information (for e.g. there is an unknown relationship between the alleged and the true fathers). In these situations, beyond the routinely used marker set, laboratories usually enlarge the number and/or the type of markers analysed. Among these, autosomal indels and X-chromosome STRs have gained popularity. The aim of this study was to compare the results obtained after complementing an initial set of autosomal STRs with indels or with X-chromosome-specific STRs in simulated paternity cases where the alleged father is a close relative of the real one. Results show that in paternity cases where a low number of incompatibilities are observed, the best strategy is to increase the number of autosomal STRs under analysis. Nevertheless, if these are not available, our study globally shows that in father-daughter duos, a set of 12 X-STRs is more advantageous than 38 highly diverse autosomal biallelic markers. Additionally, the usefulness of X-STRs was also evaluated in cases where only a close relative of the alleged parent (father or mother) is available for testing. For those situations where these markers have the power to exclude, strong LR values are obtained. In the remaining cases, LRs are usually weak and sometimes the results are more likely under the wrong kinship hypothesis.