US forensic Y-chromosome short tandem repeats database

MPKin-YSTR: Interpretation of Y chromosome STR haplotypes for missing persons cases

Y chromosome Short Tandem Repeat (STR) haplotypes have been used in assisting forensic investigations primarily for identification and male lineage determination. The current SWGDAM interpretation guidelines for Y-STR typing provide helpful guidance on those purposes but do not address the issue of kinship analysis with Y-STR haplotypes. Because of the high mutation rate of Y-STRs, there are complex missing person cases in which inconsistent Y-STR haplotypes between true paternal lineage relatives will arise and cases with two or more male references in the same lineage and yet differ in their haplotypes. Therefore, more useful methods are needed for interpreting the Y-STR haplotype data. Computational methods and interpretation guidelines have been developed specifically addressing this issue, either using a mismatch-based counting method or a pedigree likelihood ratio method. In this study, a software program, MPKin-YSTR, was developed by implementing those more sophisticated methods. This software should be able to improve the interpretation of complex cases with Y-STR haplotype evidence. Thus, more biological evidence will be interpreted, which in turn will result in more investigation leads to help solve crimes.

Linkage and linkage disequilibrium among the markers in the forensic MPS panels

For the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium. In this study, publicly accessible genomic data from five representative populations were used to evaluate the genetic linkage and linkage disequilibrium (LD) between autosomal markers represented in six major commercial panels (in total, 362 markers). Among the 3041 syntenic marker pairs, 1524 pairs had sex-average genetic distances <50 cM, and thus, these marker pairs can be considered as genetically linked. Among the 143 marker pairs with physical distances <1 Mb, 19 LD haplotype blocks (comprising 39 SNPs in total) were detected for at least one of the tested populations. Statistical methods for interpreting linked markers and/or markers in LD were suggested for various case scenarios.

Forensic investigation approaches of searching relatives in DNA databases

There are several indirect database searching approaches to identify the potential source of a forensic biological sample. These DNA-based approaches are familial searching, Y-STR database searching, and investigative genetic genealogy (IGG). The first two strategies use forensic DNA databases managed by the government, and the latter uses databases managed by private citizens or companies. Each of these search strategies relies on DNA testing to identify relatives of the donor of the crime scene sample, provided such profiles reside in the DNA database(s). All three approaches have been successfully used to identify the donor of biological evidence, which assisted in solving criminal cases or identifying unknown human remains. This paper describes and compares these approaches in terms of genotyping technologies, searching methods, database structures, searching efficiency, data quality, data security, and costs, and raises some potential privacy and legal considerations for further discussion by stakeholders and scientists. Y-STR database searching and IGG are advantageous since they are able to assist in more cases than familial searching readily identifying distant relatives. In contrast, familial searching can be performed more readily with existing laboratory systems. Every country or state may have its own unique economic, technical, cultural, and legal considerations and should decide the best approach(es) to fit those circumstances. Regardless of the approach, the ultimate goal should be the same: generate investigative leads and solve active and cold criminal cases to public safety, under stringent policies and security practices designed to protect the privacy of its citizenry.

The construction and application of a new 17-plex Y-STR system using universal fluorescent PCR

Y-chromosomal short tandem repeat (Y-STR) polymorphisms are useful in forensic identification, population genetics, and human structures. However, the current Y-STR systems are limited in discriminating distant relatives in a family with a low discrimination power. Increasing the capacity of detecting Y chromosomal polymorphisms will drastically narrow down the matching number of genealogy populations or pedigrees. In this study, we developed a system containing 17 Y-STRs that are complementary to the current commercially available Y-STR kits. This system was constructed by multiplex PCR with expected sizes of 126-400 bp labeled by different fluorescence molecules (DYS715, DYS709, DYS716, DYS713, and DYS607 labeled by FAM; DYS718, DYS723, DYS708, and DYS714 labeled by JOE; DYS712, DYS717, DYS721, and DYS605 labeled by TAMRA; and DYS719, DYS726, DYS598, and DYS722 labeled by ROX). The system was extensively tested for sensitivity, male specificity, species specificity, mixture, population genetics, and mutation rates following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The genetic data were obtained from eight populations with a total of 1260 individuals. Our results showed that all the 17 Y-STRs are human- and male-specific and include only one copy of the Y-chromosome. The 17 Y-STR system detects 143 alleles and has a high discrimination power (0.996031746). Mutation rates were different among the 17 Y-STRs, ranging from 0.30 to 3.03%. In conclusion, our study provides a robust, sensitive, and cost-effective genotyping method for human identification, which will be beneficial for narrowing the search scope when applied to genealogy searching with the Y-STR DNA databank.

Demand for larger Y-STR reference databases in ethnic melting-pot countries: Argentina as a test case

The Y chromosome behaves as a single locus. Its genetic information is useful in forensic casework, deficiency kinship testing, and population genetics studies. Continuous increases of loci number within commercial kits forced modification of worldwide reference databases. In Pan American countries, like Argentina, diverse parental ethnic groups contributed to the extant admixed urban populations. We report 509 additional haplotypes of 23 Y-STRs from donors inhabiting urban areas of six Argentinean provinces: Buenos Aires, Santiago del Estero, Santa Cruz, Rio Negro, Santa Fe, and Formosa. To better understand the demographic landscape of the admixed urban paternal lineages, structural analysis was performed using published data from other Argentinean provinces. AMOVA by Rst distance and inferred haplogroups by two predictive online software methods based on haplotypes yielded complementary results with respect to detected population structure, probably due to the different proportions of the Native American Q3-M3 haplogroup in the studied samples. This situation, which is common to most North, Meso, and South American countries, underscores the need for the additional step of typing specific SNPs for haplogroup diagnosis. We propose organizing Y-STR haplotype reference databases according to the most frequent haplogroups detected in a given admixed population.

Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines

The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.

A convenient guideline to determine if two Y-STR profiles are from the same lineage

Y chromosome STR loci are used in forensics primarily for identification purposes by determining the male lineages. The Henan province in China has established a large Y-STR (>200 000 profiles) database for criminal investigations. A large proportion of the Y-STR profiles in the database were generated using either the Applied Biosystems Yfiler(ۛ) or Yfiler(ۛ) Plus PCR Amplification kits. The additional loci in the Yfiler Plus kit as compared to the Yfiler kit results in a concomitant cumulative mutation rate increase across the loci. Therefore, in those cases when two profiles have one to a few mismatched loci, it is difficult to determine if they are from the same lineage. In this study, 7405 unrelated male profiles were manually selected from the database. Analysis showed higher power of discrimination than the corresponding Yfiler haplotypes. Further, the distributions of the number of mismatched loci and the mismatched steps were generated for father-son, grandfather-grandson, uncle-nephew, and cousins (i.e. one, two, three, and four meioses, respectively) by exhaustive pairwise comparison of the unrelated profiles using a dynamic programming approach. The same distributions were generated for unrelated pairs with mutation rates of the loci. With the distributions, the false negative and false positive rates were determined. Two Yfiler profiles with ≤2 mismatched loci or ≤2 steps are more likely from the same lineage than unrelated lineages, and two Yfiler Plus profiles with ≤4 mismatched loci or ≤5 mismatched steps are more likely from the same lineage.

Genetic analysis of 17 Y-STRs in a Mestizo population from the Central Valley of Mexico

This study aims to portray the complex diversity of the Mexican Mestizo population, which represents 98.8% of the entire population of Mexico. We compiled extended haplotype data of the Y chromosome from populations in the Central Valley of Mexico (CVM), which we compared with other Mestizo and parental (Amerindian, European, and African) populations. A complex ancestral relationship was found in the CVM population, suggesting cosmopolitan origins. Nevertheless, the most preeminent lineages point toward a European ancestry, where the R1b lineage was most frequent. In addition, important frequencies of Amerindian lineages were also found in the Mestizo sample studied. Interestingly, the Amerindian ancestry showed a remarkable substructure, which was represented by the two main founding lineages: QL54 (× M3) and M3. However, even within each lineage a high diversity was found despite the small number of sample bearers of these lineages. Further, we detected important genetic differences between the CVM populations and the Mexican Mestizo populations from the north and south. This result points to the fact that Mestizo populations present different ancestral proportions, which are related to the demographic events that gave origin to each population. Finally, we provide additional forensic statistical parameters that are useful in the interpretation of genetic analysis where autosomal loci are limited. Our findings illustrate the complex genetic background of the Mexican Mestizo population and reinforce the need to encompass more geographic regions to generate more robust data for forensic applications.

Structure and polymorphism of 16 novel Y-STRs in Chinese Han population

Y-chromosome short tandem repeats (Y-STRs) are useful tools for identifying paternity origin and male-female mixed samples because of their male-specificity, haploid inheritance and relatively simplicity. We focused on novel Y-STRs deposited in the human Genome database from DYS708 to DYS726. We typed 16 male-specific Y-STRs from males of a Chinese Han population residing in Shanxi Province (north China), including DYS708-719, DYS721-723, and DYS726, but failed in typing DYS720, DYS724 and DYS725. The 16 Y-STRs, with mean gene diversity (GD) of 0.79, included three trinucleotide Y-STRs (711, 718, 719), nine tetranucleotide STRs (708, 709, 710, 712, 713, 715, 722, 723, 726) and four pentanucleotide repeat STRs (714, 716, 717, 721). DYS712, consisting of eight alleles, was the most informative STR in our population, with a GD of 0.843. The STRs were classified as simple STRs and complex STRs, according to their structures based on sequencing. Genetic indexes, including allele frequencies, haplotype distribution and male-specificity were determined. The Y-STRs, especially those male-specific, tetra- and penta-nucleotide, with only one copy on Y-chromosome, and relative simple structures, such as DYS709, DYS714, DYS715, DYS716, DYS718, DYS719, and DYS726, were suggested for the future forensic DNA analysis, while DYS724 and DYS725 were not recommended for their multi-copy distribution. The population data provided putative Y-STRs for future genetic and forensic applications.

Developing criteria and data to determine best options for expanding the core CODIS loci

BACKGROUND

Recently, the Combined DNA Index System (CODIS) Core Loci Working Group established by the US Federal Bureau of Investigation (FBI) reviewed and recommended changes to the CODIS core loci. The Working Group identified 20 short tandem repeat (STR) loci (composed of the original CODIS core set loci (minus TPOX), four European recommended loci, PentaE, and DYS391) plus the Amelogenin marker as the new core set. Before selecting and finalizing the core loci, some evaluations are needed to provide guidance for the best options of core selection.

METHOD

The performance of current and newly proposed CODIS core loci sets were evaluated with simplified analyses for adventitious hit rates in reasonably large datasets under single-source profile comparisons, mixture comparisons and kinship searches, and for international data sharing. Informativeness (for example, match probability, average kinship index (AKI)) and mutation rates of each locus were some of the criteria to consider for loci selection. However, the primary factor was performance with challenged forensic samples.

RESULTS

The current battery of loci provided in already validated commercial kits meet the needs for single-source profile comparisons and international data sharing, even with relatively large databases. However, the 13 CODIS core loci are not sufficiently powerful for kinship analyses and searching potential contributors of mixtures in larger databases; 19 or more autosomal STR loci perform better. Y-chromosome STR (Y-STR) loci are very useful to trace paternal lineage, deconvolve female and male mixtures, and resolve inconsistencies with Amelogenin typing. The DYS391 locus is of little theoretical or practical use. Combining five or six Y-chromosome STR loci with existing autosomal STR loci can produce better performance than the same number of autosomal loci for kinship analysis and still yield a sufficiently low match probability for single-source profile comparisons.

CONCLUSION

A more comprehensive study should be performed to provide the necessary information to decision makers and stakeholders about the construction of a new set of core loci for CODIS. Finally, selection of loci should be driven by the concept that the needs of casework should be supported by the processes of CODIS (or for that matter any forensic DNA database).

Pedigree likelihood ratio for lineage markers

Lineage-based haplotype markers (e.g., Y chromosome STRs and mitochondrial DNA sequences) are important adjunct tools to the autosomal markers for kinship analysis and for specialized kinship applications such as database searching. Traditionally, the prosecution or kinship hypothesis considers the haplotypes in the same lineage and the probability of genotype data given the lineage hypothesis is simply set at 1 if the number of mismatched loci or nucleotides between the questioned person and the references is less than a predefined threshold. In this study, a kinship hypothesis based on a fixed relationship of the questioned person in the reference family is introduced. A graphical model is proposed to calculate the probability of the genotype data given the kinship hypothesis, which is the product of haplotype frequency of the founder in the pedigree and the transmission probability from the founder to all descendants. Proper mutation models are suggested for Y chromosome STRs and mitochondrial DNA sequence variants (i.e., SNPs) to calculate the transmission probability. The methods to infer the genotypes of the untyped individuals in the pedigree and the computational complexity of handling these untyped individuals are also addressed. Lastly, numerical examples of the applications are given to demonstrate the kinship hypothesis and the algorithms.