Indel polymorphisms—An additional set of markers on the X-chromosome (original) (raw)

A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR

International Journal of Legal Medicine, 2012

Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility of being analysed using short amplicon strategies, which increases the ease of analysis, contributing to justify their interest in population and forensic genetics. After the advent of autosomal and uniparental genomes (mtDNA and Y chromosome), these fields of research are also focusing on the X chromosome, given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian population samples and revealed high forensic efficiency, as measured by the accumulated power of discrimination (0.9999990 was the lowest value in males and 0.999999999998 was the highest in females) and mean exclusion chance varied between 0.998 and 0.9996 in duos and between 0.99997 and 0.999998 in trios. Finally, a segregation analysis was performed using trio constellations of father-mother-daughters in order to address the transmission pattern and assess mutation rates of this type of markers.

X-linked insertion/deletion polymorphisms: forensic applications of a 33markers panel

International Journal of Legal Medicine, 2010

Insertion/deletion (INDEL) polymorphisms are diallelic markers with potential characteristics for use in forensics and biological anthropology, including: the simplicity of laboratory analysis, the possibility of genotyping many markers in a single PCR multiplex reaction, as well as analyzing markers with special inheritance types, such as those linked to the X chromosome (X-INDEL). In this work we developed a laboratory analysis methodology using a 33-INDEL marker panel for the X chromosome in a single PCR multiplex reaction, followed by a capillary electrophoresis run. We employed the panel to genotype a sample of 351 individuals of a mixed population from the Brazilian Amazon. The results demonstrate that the measurement of biostatistical parameters for forensic use in this population is compatible with prior estimates from other populations using current X-STR panels.

Spanish allele and haplotype database for 32 X-chromosome Insertion-Deletion polymorphisms

Forensic Science International: Genetics, 2020

X-chromosome markers have been proved to be decisive both complementing and solving kinship analysis, particularly when autosomal markers are not able to produce adequate likelihood ratios between different hypothesis. On the other hand, Pereira et al., (2012) have demonstrated that 32 Insertion/Deletion (InDel) markers located on the X-Chromosome have a very important power of discrimination in human populations, being a novel tool in the forensic and population fields. So, the aim of the present work was testing the forensic and population genetic efficiency of the 32 X-InDel polymorphisms in the Spanish population, and subsequently build an allele/haplotype frequencies database. To accomplish this objective, a total of 555 samples comprising male individuals from 13 Spanish regions were analysed for the above mentioned 32 X-InDels in two independent laboratories. A pairwise F ST analysis was performed in order to understand if the studied Spanish sub-populations present significant differences among them, detecting possible population substructure. Also, linkage disequilibrium analyses were computed to investigate the presence of association between markers in the Spanish population. After Bonferroni correction, the absence of significant differences among the studied regions supports a global Spanish population database. Concerning LD, besides previously reported linked markers MID356-MID357 and MID3690-MID3719-MID2089, we also detected significant association between MID3703-MID3774, even after Bonferroni correction. Finally, after computing allele and haplotype frequencies, forensic efficiency parameters were calculated (PD males = 99.999976 %; PD females = 99.99999999998 %). Mean exclusion chance values for duos were 0.999 and trios 0.99999. These results reinforce the suitability of the 32 X-InDels marker set both in identification and kinship studies.

Study of insertion-deletion polymorphisms (indels) in the UAE population

Forensic Science International: Genetics Supplement Series, 2019

Insertion-deletion polymorphisms (indels) have been used less in forensic identification of individuals in comparison to short tandem repeat (STR) and single nucleotide polymorphism (SNP) systems. The use of indels has many advantages including low costs, simple typing methods as well as a small amplicon size of under 160 bp making them suitable for genotyping highly degraded DNA. They can also be valuable as a complementary tool to help resolve kinship cases, with the advantage of lower mutation rates when compared to STRs. The main objective of this study was to investigate the polymorphism of 30 indel loci in the UAE population and to evaluate its suitability for forensic applications. The Qiagen Investigator ® DIPplex kit was used to amplify 30 biallellic indel loci and the amelogenin locus in 500 blood samples. This technique was robust, relatively simple, and the results were analysed using the same capillary electrophoresis equipment and software used for STR typing. Allele frequencies were evaluated and forensic parameters (match probability, power of discrimination, polymorphism information content, power of exclusion and typical paternity index) were estimated for the 30 autosomal indel loci. No significant departure from Hardy-Weinberg equilibrium (HWE) expectations were observed for most of the indel loci analyzed in the samples obtained from the UAE population. The combined power of discrimination (CPD) and combined match probability (CMP) values were 0.999999999999754 and 2.46 X 10-13 , respectively, which indicated that the 30 indel loci are highly polymorphic and are appropriate for forensic human identification purposes. Even when the match probability of STRs was low, indels gave an acceptable value for forensic application.

Genetic characterization of 32 X-InDels in a population sample from São Paulo State (Brazil)

International Journal of Legal Medicine, 2019

X-chromosomal markers can be useful in some forensic cases, where the analysis of the autosomal markers is not conclusive. In this study, a population sample of 500 unrelated individuals born in São Paulo State was characterized for 32 X-InDel markers. No deviations from the Hardy-Weinberg equilibrium were detected, except for MID1361. The 32 X-InDels showed an accumulated power of discrimination of 0.9999999999993 in females and 0.99999993 in males and an exclusion chance of 0.999996 in trios and 0.99995 in duos. São Paulo showed lower genetic distances to the Colombian admixed and European populations than to Native American, Asian, or African populations. Ancestry analysis revealed 41.8% European, 31.6% African, and 26.6% Native American contributions. Segregation analysis was performed in 101 trios, and the mutation rate was estimated to be low.

Usefulness of X STR Haplotype markers in Forensic DNA Profiling

Haplotype is a lineable combination of alleles at multiple loci that are transmitted together. The importance and application of these haplotypes has been gradually increased in forensic sciences. After Y STR's on Chromosome Y and Mitochondrial DNA now the current focus is on haplotype study involving X STR's on Chromosome X. Fathers transmit their X chromosome to daughters as haplotypes. The X-chromosome is 155 million base pairs (Mb) long and carries approximately 1250 known genes. Women carry two copies of X chromosome while men are hemizygous for all X chromosomal markers. Research findings suggest that Mutations on the X chromosome occur less frequently than on autosomes. The analysis of X-chromosome markers can be valuable in particular situations, for example, deficiency kinship cases, where the putative father cannot be typed. X-chromosome short-tandem repeats (X-STRs) are widely used in forensic genetics. X chromosome-linked short tandem repeat (X STR) analysis have been used in paternity testing, more complex deficiency paternity cases, when half-sisters and/or grand mothers are to be examined; paternity testing including blood relatives; and rare cases of maternity testing. Its usefulness is also seen in cases when female DNA traces have to be analized against a male background which is more common in the case of sexual assault with children. In present paper the utility of X STR is presented along with a pilot database of a tribal population of Bhil from Madhya Pradesh, to establish frequencies for the single STRs and their haplotypes in Indian population.DNA isolation was done by automated DNA extraction system 12GC from PSS Japan, DNA was quantified using real time PCR ABI 7000 and X STR profiles were generated using Investigator Argus X-12 amplification kit on ABI 3100 genetic analyser. The work was done with the financial support from Madhya Pradesh council of Science and Technology, Bhopal (MP) India.