Usefulness of X STR Haplotype markers in Forensic DNA Profiling

Author Name(s): *Pankaj Shrivastava,Toshi Jain, Veena Ben Trivedi
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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.


Forensic, DNA Fingerprinting, X STR, DXS10148, DXS10135, DXS8378, DXS7132, DXS10079, DXS10074, DXS10103, HPRTB, DXS10101, DXS10146, DXS10134, DXS7423.


Application of autosomal and Y-chromosomal STR markers forensic investigation is in routine practice now. In some kinship analyses involving maternal relatives, mitochondrial DNA analysis is also being used. But the use of mitochondrial DNA analysis is still not that common and most of the forensic laboratories are not doing mitochondrial DNA analysis because of the fact that protocol of genotyping is comparatively easier and also ready to use pre validated multiplex markers are available. In case of mitochondrial sequencing situation is not the same. Use of X-chromosomal short tandem repeats (X-STR) loci is also started for forensic practice in some complex kinship cases. The commercially available kit of Investigator Argus X-12 (Qiagen, Hilden, Germany) makes it possible to examine the markers belonging to four linkage groups of X-chromosome, linkage group 1: DXS10148-DXS10135-DXS8378, linkage group 2: DXS7132-DXS10079-DXS10074, linkage group 3: XS10103-HPRTB-DXS10101 and linkage group 4: DXS10146-DXS10134-DXS7423 in a single PCR. The availability of Argus X-12 Kit for simultaneous amplification of twelve X-STR loci has created increasing interest among forensic scientists for analyzing X STR markers. Statistical parameters obtained in different studies on X-STR indicate their usefulness in forensic genetics investigations. A large number of short tandem repeat (STR) markers on the entire human X chromosome have been described and established for use in forensic genetic testing [1]. These markers located on X chromosome have a particular inheritance pattern: women are dizygous and men are hemizygous, with the latter receiving the single X from the mother similarly father transmit their X chromosome to daughter as haplotypes. Analysis of X-chromosomal loci might be beneficial in deficiency paternity cases, where half-sisters and/or grandmothers are examined [2]. True daughters carry always the whole paternal X-chromosome (ChrX) and therefore both of the daughters ChrX haplotypes can also be completely recognised when a father and his daughter are submitted to a jointed typing. Likewise, jointed ChrX typing for a mother and her son reveals also both of the maternal haplotypes. The latter, however, applies with a high certainty only to closely linked loci [3–7]. Due to their particular mode of inheritance, X STRs often allow easy and informative haplotyping in kinship analyses, Moreover, some X-STRs are known to be tightly linked so that, in combination, they constitute even more complex genetic markers than each STR taken individually. As a consequence, X-STRs have proven particularly powerful in solving complex cases of disputed blood relatedness [1]. And can serve as a complement to autosomal STRs and mitochondrial DNA polymorphism [8]. Research findings suggest that Mutations on the X chromosome occur less frequently than on autosomes due to several times lower nucleotide mutation rate in women than in men, which also reduces the X chromosome genetic diversity[9]. Although a considerable amount of information on polymorphism and pairwise genetic distance (Fst) based on the allele frequencies have been carried out in the past few years in different parts of the world on X STR markers [10-18]. But, there exist still a lacuna for this type of study on Indian populations. The present study is an attempt to create a pilot X-STR database with comparative allelic distribution of each locus in population of the Bhil tribes of Madhya Pradesh, India, by using Investigator Argus X-STR 12 kit (Qiagen, Hilden, Germany) which will be helpful not only in criminal investigation such as personal identification and kinship testing but for other anthropological purposes as well. This is first pilot study on the population of Bhil tribes of India. A case of paternity inclusion and exclusion is also presented to show case the utility of X-STR 12 marker multiplex kit for its use as autosomal markers in cases where paternity of female child is in question. It can also be used to confirm the paternity and/maternity of the child where in one or two locus a mismatch is observed with autosomal STR.


This is the first report of X-STR data on Bhil population of Madhya Pradesh state of India. The created population data base allows the STR markers included in the Argus X-12 Kit to be applied in routine case work. High values of the forensic statistical parameters combined with in dependent inheritance of the studied loci make them a very useful marker set for forensic genetics investigations. Application of X-STR loci may constitute a valuable addition to autosomal markers, particularly in complex kinship and paternity cases, e.g. when instead of the alleged father, his mother (i.e. the putative grandmother of the child) is the source of the reference DNA sample.

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