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A Review on Y-chromosome STR haplotyping

Umesh Sharma1 Author

Department of Forensic Science, Galgotias University, Greater Noida

Sahiba Lall2 Corresponding Author

School of Biosciences, Department of Biotechnology Lovely Professional University

Dr Rajeev Kumar2 Supervisor

Department of Forensic Science (School of Basic & Applied Sciences) Associate Professor

Abstract

The area of forensic Y chromosome analysis has been successfully developed to become standard in laboratories working in criminal casework all around the world since the early 1990s. Because of their capacity to detect male- specific DNA, highly variable Y-chromosomal polymorphisms, also known as STR sequences, are an important addition to the conventional panel of autosomal loci used in forensic genetics. The Y chromosome's male-specificity makes it particularly beneficial in cases of male/female cell mixing, such as in sexual assault cases. On the other hand, because male relatives have an identical Y-STR profile for numerous generations, haploidy and patrilineal inheritance complicate the interpretation of a Y-STR match. Because paternal relatives tend to dwell in their ancestors' geographic and cultural domain, Y chromosome research offers the ability to identify the population of origin of a DNA profile. The fields of application of Y chromosome haplotyping, the interpretation of results, databasing initiatives, and population genetics aspects are all included in this study.

Keywords: Y-STR, Y chromosome haplotyping, DNA profile, Y-chromosomal polymorphisms.

Introduction

Almost all multicellular organisms have sex-chromosomes, which play an important role in determining sex [1]. In mammals, the Y-chromosome is one of two sex-chromosomes and is usually the karyotype's smallest chromosome [2]. Because of its distinctive properties, such as a long non-recombining region and a holandric inheritance pattern, the Y-chromosome is ideal for researching evolutionary relics, speciation, and male infertility and/or subfertility.

The Y chromosome's features read like a list of exceptions to human genetics' rules: it is not required for life (males

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have it, but females do OK without it), half of it is tandemly duplicated SATELLITE DNA, the remainder contains few genes, and most of it does not recombine [4,5].

The human Y-chromosome is known to be susceptible to mutation, with male selectivity, haploidy, and the ability to avoid cross-over [6]. Y-STRs have been frequently employed in forensic DNA testing, such as identifying persons from stains of male/female DNA mixes and paternal pedigree study [7]. Furthermore, Y-chromosomal haplotypes provide invaluable insights into anthropology, genealogy, and population genetics [8]. As a result, a variety of commercially available Y-STR kits were utilised to provide a variety of population Y-chromosomal data and establish the Y-STR reference databases. In this review, we’ll talk more about the Y-STR.

Y chromosome STR typing

The Y chromosome, on the other hand, is such a great instrument for studying recent human evolution from a male perspective, and it plays specialised but significant functions in medical and forensic genetics because of its disdain for the laws [9]. The Y chromosome must be investigated differently than the rest of the genome [10]. Physical analyses are more important than genetic mapping in the absence of RECOMBINATION, therefore the near- complete sequence of the EUCHROMATIC regions of the chromosome may have an even greater impact here than on the remainder of the genome [11].

The use of STR markers to haplotype the human Y chromosome, also known as Y-STR haplotyping, is a method for detecting and distinguishing male DNA [12, 13, 14]. The technology was developed concurrently with autosomal STR analysis for human identification and evaluated in a similar manner for forensic analysis [15]. The utility of the first Y-chromosomal STR polymorphism in crime casework was established shortly after its definition and evaluation when a mixed stain from a vaginal swab of a raped and murdered female victim was resolved by Y-STR analysis and an unjustly convicted male was removed [16]. The principal use of forensic Y-STR haplotyping is still the unambiguous detection of the male component in DNA mixtures with high female background. In sexual assault situations, Y-STRs in combination with autosomal STRs will be used preferentially [17]. Y-STRs and Y-SNPs can provide intelligence information about the ethnic origin of a male DNA donor, and the method has been beneficial in reconstructing paternal relationships, for example, in mass disaster investigations [18].

Even though a crime sample fits a suspect's Y-STR profile, patrilineal relatives of the suspect cannot be ruled out as the stain's donor [19]. As a result, unlike autosomal STRs, evaluating a Y-STR match requires access to reference databases that capture the variance and relatedness of haplotypes within local populations [20]. Because of the differences in underlying population structure, merging information from lineage genetic markers like the Y- chromosome (or mitochondrial DNA) with data from meiotically recombining loci (autosomes) into a single likelihood ratio is often inconclusive and should be avoided [21].

Y-STRs have been chosen from a pool of potential sequences in the same way that autosomal STRs have been. The markers of choice were mostly tetrameric repeats, with an average repetition number of 10 to 30 yielding small amplicons in the PCR [22]. In all significant metapopulations, the discrimination power must be quite high, and the

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use based on these parameters. The ISFG DNA commission's proposals are currently gathering momentum for a panel of up to 17 extensively assessed markers (Table 1) in practical use (International Society of Forensic Genetics) [23]. The recommended core STRs are all present in commercially available Y-STR kits, which contain between 9 and 17 loci. Additional Y-STR loci are being screened and assessed in order to expand the core marker sets [24].

The Y-STR haplotyping method has been tested and standardised across labs, and it is currently commonly utilised in forensics [25]. The goal of Y-STR loci is not to replace any of the core autosomal loci, but to provide a different tool that can provide information that would otherwise be unavailable in a variety of situations:

1. For mixed stains containing a higher proportion of female DNA than male DNA (which is frequently observed in vaginal swabs collected after sexual intercourse).

2. When testing for seminal fluid or sperm is negative in cases of suspected sexual assault.

3. In cases of sexual assault where the evidence is positive for semen but no DNA from the victim can be found, or probable male alleles are below the autosomal STR detection threshold.

4. In situations of sexual assault if the evidence is amylase-positive and a male/female mix is predicted (e.g., traces of kisses or bites).

5. In circumstances where the majority of sperm cells are suspected of being destroyed and differential lysis is futile or dangerous.

6. In situations of sexual assault requiring the screening of a significant number of sperm or other stains.

7. When it comes to determining the number of male donors in a stain.

8. In circumstances when a male perpetrator's cells are believed to be present in the evidence (e.g., female fingernail hyponychium where male biological material may accumulate after violent attacks).

9. In circumstances when a stain donor's patrilinear kinship must be established.

10. In circumstances where the population of origin of the stain donor must be inferred.

Figure.1: Y-STR forensic core set characteristics [3].

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For DNA mixture analysis, Y-STR haplotyping

One issue with using PCR for DNA typing is that it fails to amplify the small component in DNA mixes with very uneven heterogeneous DNA ratios. The buildup of PCR products from alleles of the large component causes allelic dropout, masking, or suppression of the amplicons of the minor component. For autosomal mixes, the minor component is often undetectable below a ratio of 1:25–1:50 [26].

Y-STR typing can minimise or reduce this diagnostic gap, particularly in combinations with a low male component and a significant female background, which is a common condition in vaginal swabs tested after suspected sexual assault. DNA quantities of [1000 ng were commonly found in non-differentially extracted vaginal swabs, with the bulk coming from female DNA] [27]. A series of investigations on non-probative samples with significantly uneven male and female DNA ratios have been published in the previous ten years [28]. Model tests showed that a tiny Y- STR tetraplex with 0.4 ng male DNA as the minor component could identify the minor male component in male/female mixtures up to a ratio of 1:4000. Other authors report successful typing in ratios as high as 1:3000 using 1 ng male DNA amplified in a triplex or 1:600 using a hexaplex with 0.5 ng male DNA [29, 30]. The design of the multiplex PCR, its sensitivity limit, and the concentration of the minor component all influence the performance of Y-STR typing in mixtures [31].

Multiplex kits now on the market contain between 9 and 17 Y-STR markers, with detection limits of less than 0.1 ng DNA. With artificial blood stains on cotton (18 cells per PCR), for example, analysis with the Power- PlexOY system (12 markers) provided clear results and incomplete profiles (65% drop out of markers) with only two cells [32]. Y-STR analysis of casework-related samples has been examined in a number of journals in addition to experimental mixing investigations. Sibille et al. found positive Y-STR results in almost one-third of the re-tested sexual assault cases where the swabs were re-tested [33].

Initially classified as "negative" for sperm. Dekairelle and Hoste reported a 48 percent success rate using Y-STR haplotype analysis for PSA (prostate-specific antigen) positive differentially extracted swabs that did not yield a result using autosomal STRs in another systematic study [34].

Results of Y-chromosomal STR profiling and their interpretation

In theory, the three possible interpretations of a diploid DNA profiling result, including matches (or inclusions), exclusions, and inconclusive outcomes, also apply to Y-STR haplotypes [35]. However, because Y-STR DNA profiles are lineage-specific rather than individual-specific, the significance of matches differs from that of autosomal markers. Because of the lack of recombination, the Y-chromosome (which includes all STRs currently used in forensic genetics) functions as a single locus [36].

As a result, the autosomal markers" product rule" cannot be used to determine the population frequency of a Y-STR haplotype, and huge reference databases must be employed instead. The power of discriminating of Y-STRs is poor when compared to autosomal STRs, as seen by haplotype frequencies found in or extrapolated from these databases, which typically vary between 10 and 10-5 [37, 38].

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● The counting method

● The ‘‘haplotype surveying’’ method

When paternal relatedness is a factor in a criminal case, Y-STR haplotyping can be helpful. Detlaff-Kakol and Pawlowski report an imposing example in which the criminal was identified using the Y-STR typing of a broad population. DNA profiles retrieved from semen stains left at crime scenes revealed that all of the rapes were committed by the same individual. A huge number of suspects were eliminated using the Y-chromosome haplotype (nine loci) that was acquired [39].

One individual was discovered to have the same DNA profile in all Y-chromosome STR sites studied and shared common alleles in nine of ten autosomal loci, strongly implying that the real rapist and the typed man were related males. The autosomal STR profile found at the crime scenes was identical to that found in reference to DNA taken from the man's brother. With the normal use of Y-chromosome typing in forensic casework, cases like these with Y- STRs providing information on paternal relatedness of tested persons are projected to become increasingly common [40].

The capacity of Y-linked markers to reveal the population origin of a male person will become increasingly useful when Y-STR haplotyping becomes more popular due to the availability of commercial kits and appropriate population databases. Not only do distant metapopulations like Africans or European isolates like Finns, Sami, or Roma have different modal Y-STR haplotypes, but so do recently divergent neighbouring groups like Eastern Slavic or Romance-speaking Europeans. This information can be useful in determining a stain donor's paternal population of origin in non-suspect situations or when identifying decomposing bodies or skeletal remains [41, 42].

Problem formulation

1. Y-STR haplotyping is a technique for detecting and distinguishing male DNA. Y-STRs are a valuable supplement to the typical panel of autosomal loci used for DNA profiling, particularly in mixed-sample instances.

2. Because male relatives have an identical Y-STR profile for numerous generations, haploidy and patrilineal inheritance complicate the interpretation of Y-STR haplotype matches. In order to evaluate the level of haplotype sharing in a reference population, large structured databases are required for the assessment of match probability.

The counting method, which requires a vast database of worldwide sampled populations, is the most conservative and simplest defendable strategy to reporting a Y haplotype match. The Y-STR Haplotype Reference Database (YHRD) was created for this purpose.

3. Because paternal relations are more likely to live in their ancestors' geographical and cultural domain, Y chromosome analysis has the potential to determine the population of origin of a specific Y chromosomal profile.

4. Currently, crime labs employ a panel of approved Y-STR markers. If information other than the Y chromosome is not available, this core marker set will undoubtedly need to be supplemented with other highly informative loci to confirm or rule out a match.

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