1. INTRODUCTION

India has the greatest polygenetic population of any secular nation. Known to be a cultural melting pot, India is home to people of many different languages, cultural backgrounds, and religious traditions [1]. There are 4693 recognized demographic subgroups in India. They are comprised 2205 recognized communities, 589 subgroups, and 1900 separate administrative regions [2]. South India consists of the Indian regions of Andhra Pradesh, Karnataka, Kerala, Tamil Nadu, and Telangana, as well as the Union territories of Lakshadweep and Puducherry. As of April of 2020, there were 253,051,953 people living in 635,780 km² or 245,480 sq miles [3]. The western part of India includes the states of Maharashtra, Rajasthan, Gujarat, and Goa. As of April 2020, there were 173,343,821 people living in 508,032 km² or 196,152 sq miles [4].

Forensic scientists now commonly utilize DNA analysis based on short tandem repeats (STRs) to determine paternity and to examine more complex criminal cases, such as those involving rape, murder, and mass rape [5]. Due to their high diversity and widespread distribution throughout the human genome, short tandem repeats (STRs) are useful genetic identifiers for identifying specific people. Multiplex polymerase chain reaction (PCR) has made it possible to amplify numerous loci at once, making STR typing a viable tool for human identification [6]. Autosomal STR loci are widely employed in forensics and paternity testing [7,8]. The odds of two unrelated people having identical STR profiles, or fingerprints, are “about one in 57 trillion,” as shown by the frequencies of the STR alleles [9]. Several nations now have their own forensic DNA databases. To prove the identification of missing individuals, victims, criminals, under trial, unknown dead persons, etc., the “DNA Technologies (Use and Application) Regulation Bill – 2019” was drafted in India. The Bill includes language creating a DNA Regulatory Board (DRB) charged with performing the duties and exercising the authority specified in the Bill. The national forensic DNA database for the purpose of identifying the aforementioned class of individuals will be maintained through the establishment of National and Regional DNA Data Banks, which are also provided for in the bill. This will help improve the scientific level and efficiency of DNA testing in the India [10]. The Indian government is now debating the bill, which is evidence that a comprehensive regional and state-level DNA database is necessary. studied genetic polymorphism of 15 STR loci in 123 unrelated individuals of Madhya Pradesh population and evaluated autosomal STR diversity and forensic important parameters. They concluded that locus Penta E showed the highest power of discrimination (0.978) the highest polymorphism information content (0.900) and also suggested all loci are highly polymorphic, showed significant genetic diversity, and have the potential for forensic application carried out the research to investigate the genomic diversity and population structure in the Muslim community of Telangana using 23 autosomal STR in 184 randomly selected unrelated healthy individuals and concluded that locus SE33 showed 37 observed alleles, which is the highest number of observed alleles among all the studied loci and SE33 showed the highest number of observed alleles (37) among all the studied loci. The locus SE33 was the most polymorphic and discriminatory locus and may be useful for forensic application. Similar to these studies, lot of research had been done using STR focusing on specific community such as Muslim community of Telangana, Teli population of Maharashtra, Mina, Gujjar, and the admixed population of Rajasthan and Sikh population of central India. In this research, it is attempted to cover two regions of India (South and West) and also compared their genetic parameters and frequency that can be applied in forensic application. In India to prove the identification of missing individuals, victims, criminals, under trial, unknown dead persons, etc., the ”DNA Technologies using STR has not been used as prevalent as in other countries. The objective of the research was to determine the allele frequencies and statistical parameters for medicolegal interest of 15 loci Penta E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179, Vwa, Penta D, CSF1PO, D16S539, D7S820, D13S317, and D5S818 in subjects with a large population of unrelated south and West Indian population. In this research, 410 buccal swab samples were collected from unrelated individuals of south and West Indian states after getting their informed consent forms. From the collected samples, DNA was extracted and stored in –21°C. The extracted DNA samples were quantified to analyze their DNA concentration by measuring the absorbance at 260 nm (A₂₆₀) in a spectrophotometer using a quartz cuvette. The quantified DNA was ready to be used for the DNA amplification. Next, amplification process was carried out using PP16 multiplex primer. The amplified PCR samples were engaged into DNA sequencing using ABI Applied BioSystem 3130 sequencer. Once the samples were sequenced, the data were analyzed with the use of GeneMapper software and, subsequently, the frequency and forensic significant parameters calculated using the FORSTAT software. The maximal allele frequency at TPOX was found to be 0.4976 in the South Indian population, 0.4925 in the West Indian population, and 0.5040 in the combined South and West Indian population, respectively. The sequence-based allelic frequencies for south and West Indian population groups studied here with STR would enable equipped laboratories to use the frequencies and forensic important parameters obtained from this study for relationship or forensic identification. This work complements other available sequence-based allelic frequency databases published by other studies carried out in South and West Indian states, but also fills a large data gap for the South, and West Indian populations. In addition, the similarities and differences have been compared between these two populations that would enable forensic and relationship testing industry to use these parameters confidently when analyzing live forensic cases are done using STR for any type of paternity, maternity, missing person analysis, etc. The key limitations from the previous studies were to collect the samples from different parts of the states in India and high expenses to analyze the more number of samples. The advantage of this study aside from being the new approach to compare the South and West Indian population with 15 STR loci and it can also be used by the DNA analysts in South and West Indian laboratories for live forensic and relationship casework, as well as for further research outside.

2. MATERIALS AND METHODS

Buccal swab samples of 410 healthy unrelated individuals 209 (123 males and 86 females) and 201 (108 males and 102 females) between the age group of 17 and 23 from South and West Indian states were collected respectively after getting their informed consent [Figure 1]. The work was authorized by the Ethics Committee of SRM Institute of Science and Technology–Chennai. (1887/IEC/2020).

Figure 1: South and West Indian states from which the samples were collected. [Click here to view]

3. RESULTS

The allele frequencies calculated for South, West, and combined South and West Indian population are given in Tables 1-3, respectively.

Table 1: Allele frequencies in South Indian population.

Table 2: Allele frequencies in West Indian population.

Table 3: Allele frequencies in combined South and West Indian population.

Minimum allele frequency of 0.0024 was found in different alleles which are mentioned below:

D3S1358-20 TH01-5, D21S11-26, 29.2, 33, 34, and 36 D18S51-15.2 and 24 Penta E-15.4, 21 and 22 D13S317-15 D16S539-5 and 15, CSF1PO-15 D18S1179-9 TPOX-6,7, and 13 FGA-19.2, 20.2, 22.2, and 30.

Minimum allele frequency of 0.0025 was found in different alleles which are mentioned below:

D3S1358- 12 TH01-11, D21S11- 25 D18S51-13.2 and 14.2 Penta E-22 and 23 CSF1PO-8 Penta D- 3.2, 6, 7 and 17 Vwa- 11 D8S1179-9 and 18 TPOX-7 FGA-17, 17.2, 22.2, 25.2, 28, 29, and 30.

Minimum allele frequency of 0.0010 was found in different alleles which are mentioned below:

D3S1358- 20 TH01-5, 11, D21S11-29.2, 30.3 and 34.2 D18S51-24, D16S539-5,15 Penta D-3.2, 17 Vwa-12, D8S1179-18, TPOX-13, and FGA 17,19.2,25.2,30.2, and 33.2.

By comparing the alleles in the population groups, the following alleles 15.2, 15.4, 18.2, 19.2, 20.2, 29.2, 33.1, 34, 35, and 36 were observed in South Indian while they were not found in the West Indian population; whereas the alleles 3.2, 13.2, 14.2, 17.2, 20.3, and 25.2 were recorded in the West Indian population but were not observed in the South Indian population. On the other hand, the following alleles 10.3, 15.3, 16.2, 21.2, and 23.2 were found in the combined population but were not seen either in South or West Indian population.

A total of 157, 159, and 182 alleles were recorded in the South, West, and combined South and West Indian populations, respectively. Alleles were counted, and the corresponding numbers were 46, 42, and 54. In TPOX, the allele frequencies in the South Indian population varied from 0.0024 to 0.4976, those in the West Indian population from 0.0024 to 0.4925, and those in the combined Indian population from 0.0010 to 0.5040. TPOX locus had the highest frequency in all three sample populations. Allele frequencies varied from 6 (D7S820) to 18 (Penta E) in the South, 7 (THO1, D7S820, D16S539, and TPOX), to 19 (Penta E) in the West, and 8 (TH01, D13S317, D7S820, and TPOX) to 23 (FGA) in the South and West Indian population combined. The West Indians had the highest frequency of alleles at the FGA locus (19/42=45.2%), followed by the combined South and West Indian population also at the same FGA locus (23/54=42.6%), whereas the South Indians had at the Penta E locus (18/46 = 39.1%).

Analyses of the range and number of alleles at each locus for the South, West, and combined Indian population revealed that the maximum range at the same locus Penta E was 5-22, 10-25, and 5-25 and the number of alleles were 18 and 19 for South and West Indian population, respectively, whereas the FGA locus recorded the maximum of 23 alleles in the combined Indian population.

Most common allele (MCA) and least common allele (LCA) observed at different loci are given in Table 4.

Table 4: MCA and LCA alleles in South, West, and combined Indian populations.

The least common alleles occurred in many of the loci only one time.

The polymorphism values of STRs expressed by various statistical parameters are presented in Tables 5 for south, west, and combined Indian population.

Table 5: Statistical parameters of STR loci for South, West, and combined South and West Indian population.

According to the above data, the lowest match probability was 0.0444, 0.0710, and 0.0343 in PENTA E in the South, West, and combined Indian populations, respectively, while the corresponding highest match probability was 0.1906, 0.2005, and 0.1805 at TPOX. The highest values of discrimination capacity were found at the locus Penta E (0.9556, 0.9290, and 0.9659) and the lowest values at the locus TPOX (0.8094, 0.7995, and 0.8157) in South, West, and combined Indian populations, respectively.

The lowest polymorphic information content (PIC) values were 0.6039, 0.5935, and 0.6074 at locus TPOX in the South, West, and combined Indian populations, respectively, and the corresponding highest values were 0.8940 and 0.8916 at Penta E in the south and combined Indian populations, and 0.8516 at locus D18S51 in the west.

In the South, West, and combined Indian populations, the lowest expected heterozygosity (Hexp) values were 0.6503, 0.6475, and 0.6499, respectively, at the locus TPOX, and the maximum values of 0.9017 and 0.8988 at locus Penta E were recorded in South and combined Indian populations and 0.8658 in the locus D18S51 in the West Indian population. The minimum observed heterozygosity (Hobs) values were 0.6464, 0.6550, and 0.6510 in the South, West, and combined Indian populations, respectively; whereas the corresponding maximum observed heterozygosity values were 0.9071 and 0.8857 in the South and combined Indian populations and 0.8600 at FGA locus in the west. The minimum homozygosity values of 0.0929 and 0.1143 were found at locus Penta E in the South and combined Indian populations, respectively, while 0.1400 was found at locus FGA in the west. Among the South, West, and combined Indian populations, the highest homozygosity values were 0.3536, 0.3450, and 0.3489, respectively at the locus TPOX. The Power of Exclusion (PE) minimum values of 0.3649, 0.3769, and 0.3675 were recorded at locus TPOX in the South, West, and combined Indian populations, respectively, whereas the corresponding maximum values of 0.8107 and 0.7731 were noted at Penta E in the south and combined Indian populations, respectively, and in the west, it was 0.7161 at FGA locus. The paternity index (PI) minimum values of 1.5106, 1.5802, and 1.5058 were observed at locus TPOX in South, West, and combined Indian populations, respectively, while the maximum values of 6.3467 and 4.5763 were observed in Penta E in the South and combined Indian populations, respectively, while in the west, it was 4.2000 in Penta D locus. In both populations, no divergence from Hardy–Weinberg equilibrium was detected (P > 0.05).

Among tables presented in this study, the frequency tables of south and west (1 and 2) Indian frequencies are the most important ones as they have been highlighted the frequency of South and West Indian population separately which can be used to potential relationship analysis when the live samples analyzed from those states.

4. DISCUSSION

The accuracy of the findings is generally improved by gathering data from a larger sample size. Prior research revealed that calculating the probability using just 100–150 tested people per population [14]. For this reason, a total of 410 people from the South and West Indian populations were evaluated to determine allele frequency analyses and statistical parameters of forensic relevance.

5. CONCLUSION

The highest range of allele frequency was noted at TPOX for all three populations. In South, West, and combined Indian population, the observed alleles were 46, 42, and 54, respectively. The corresponding total alleles were 157,159, and 182, respectively. The range of alleles was from 6 to 23 in all three populations. These three parameters showed the South and West Indian population had similar range of observed alleles, frequencies, and number of alleles. The locus Penta E was the most variable of the studied loci, displaying the highest values of discrimination capacity (0.9659), expected heterozygosity (0.8988), observed heterozygosity (0.8857), polymorphic information content (0.8916), power of exclusion (0.7731), and paternity index (4.5763) and the lowest values of match probability and homozygosity. However, locus TPOX recorded the highest match probability (0.1805) and homozygosity (0.3489), and the lowest polymorphic information content (0.6074), expected heterozygosity (0.6499), observed heterozygosity (0.6510), power of exclusion (0.3675), discrimination capacity (0.8157), and paternity index (1.5058) indicating the least variable locus in these population. The current data may serve as a suitable starting point for building the Indian population’s DNA database. The information gathered here may supplement existing databases from other STR-based studies of Indian people. These 15 STR loci are useful for personal identification due to their specificity and polymorphism. Thus, the authors advocate for further genetic or forensic examination of polymorphism in the Indian population substructure utilizing short tandem repeat [STR]. People from the states of Lakshadweep, Pondicherry, Kerala, Tamil Nadu, Telangana, Andhra Pradesh, Karnataka, Gujarat, Rajasthan, Maharashtra, and Goa should be considered a genetically representative sample of the South and West Indian population for the purposes of genetic analysis or the establishment of a DNA database for the entire Indian population.

6. AUTHORS’ CONTRIBUTIONS

All authors made substantial contributions to conception and design, acquisition of data, or analysis and interpretation of data; took part in drafting the article or revising it critically for important intellectual content; agreed to submit to the current journal; gave final approval of the version to be published; and agreed to be accountable for all aspects of the work. All the authors are eligible to be an author as per the International Committee of Medical Journal Editors (ICMJE) requirements/guidelines.

7. FUNDING

There is no funding to report.

8. CONFLICTS OF INTEREST

The authors report no financial or any other conflicts of interest in this work.

9. ETHICAL APPROVALS

The ethical committee of SRM Institute of Science and Technology in Chennai, India has approved this study (1887/IEC/2020).

10. DATA AVAILABILITY

Data can be obtained from the corresponding author upon valid request.

11. PUBLISHER’S NOTE

This journal remains neutral with regard to jurisdictional claims in published institutional affiliation.

REFERENCES