Molecular characterization and population study of an X chromosome homolog of the Y-linked microsatellite DYS391

A newly devised multiplex assay of novel polymorphic non-CODIS STRs as a valuable tool for forensic application

DNA profiling that relies on sets of highly polymorphic autosomal STR markers is widely used in the forensic field for human identification and paternity testing. However, the number of markers that are included in the STR kits that are currently available is insufficient to conclusively prove or disprove a relationship between individuals, especially when complex family scenarios are suspected or indirect analyses are required. In these cases, it becomes necessary to increase the number of loci under analysis to reach an adequate likelihood ratio (LR). In this study, we discovered 18 new autosomal non-CODIS STR loci (D1S1616, D1S1608, D2S437, D3S2457, D4S2406, D4S3249, D5S2843, D5S2501, D6S1010, D8S1039, D12S1301, D14S586, D15S815, SHGC-145653, CHLC.GATA14D12, D1S1603, HUMUT7148, and CHLC.GATA84D07) by web scanning and experimental screening. On the basis of this discovery, we developed a novel multiplex typing system named the "SiFaSTR 21plex_NCII Typing System" comprising 1) the 18 non-CODIS autosomal STRs mentioned above, 2) a CODIS locus of D2S1338, and 3) Amelogenin and DYS391. A forensic developmental validation, including sensitivity, species specificity, concordance, reproducibility, sample suitability, testing stability, and mixture testing, was performed following SWGDAM. The results of the validation studies indicated that this system is accurate, reliable and suitable for human DNA profiling. The sensitivity study of the system demonstrated that a full profile was obtainable with DNA as low as 125 pg. Species specificity was proven by the lack of cross-reactivity with a series of common animal species. The stability study demonstrated that 1 ng of control DNA could be fully genotyped with concentrations of haematin ≤ 150 μM, indigotin ≤ 5000 ng/μl, urea ≤ 16000 ng/μl, nigrosine ≤ 100 ng/μl and humic acid ≤ 20 ng/μl. In the mixture test, all of the minor alleles could be called at mixed ratios of 1:1, 1:3 and 3:1. We also investigated the allelic frequencies and forensic parameters of the included markers in 259 Chinese Han individuals. The forensic efficiency parameters, including the total power of discrimination (TDP) and the combined exclusion power in duos (CPE_duos) and in trios (CPE_trios) of the system were calculated to be greater than 0.9999999, 0.9997347 and 0.9999997, respectively. This result proved that the system is suitable for human identification and paternity testing. The 18 newly discovered non-CODIS STRs and the developed system will be a valuable supplementary tool for the forensic community and will help solve complex paternity cases, evolutionary studies and population investigations.

Molecular sexing and population genetic inference using a sex-linked microsatellite marker in the nine-spined stickleback (Pungitius pungitius)

BACKGROUND

Sex-specific DNA markers can serve as tools for molecular sex identification, as well as for population genetic inferences. We investigated the potential utility of a microsatellite marker located on sex chromosomes for molecular sexing of Fennoscandian nine-spined sticklebacks (Pungitius pungitius). In addition, we assessed the patterns of allelic differentiation between X and Y chromosomes across the populations to examine if the sex chromosomes had been highly differentiated prior to the postglacial recolonization of Fennoscandia.

FINDINGS

A clear and consistent sex difference in allele size distribution was observed at the Stn19 locus throughout the 15 populations investigated. Males were distinguishable by the presence of distinct male-specific alleles, which were lacking in all females. There was no indication of recombination between sex and the Stn19 locus in the 647 individuals tested. The degree of genetic differentiation between the X and Y chromosomes was much higher than that of interpopulation differentiation in the respective chromosomes.

CONCLUSIONS

Our results indicate that the Stn19 locus can be used for molecular sex identification in Fennoscandian nine-spined sticklebacks. The consistent pattern of high allelic differentiation between the X and Y chromosomes in these populations suggests that the sex chromosomes were already highly differentiated prior to the postglacial recolonization of Fennoscandia.

A comparative analysis of two different sets of Y-chromosome short tandem repeats (Y-STRs) on a common population panel

A comparative analysis of two Y-STR loci sets was conducted on a population sample of 224 individuals, 114 Caucasians and 110 African Americans. One set of loci, designated the OSU 10-locus set, comprises variable, single copy, male-specific loci that are dispersed across the Y-chromosome. Parallel evaluations were performed using the 10 Y-chromosome loci most frequently used for forensic analysis, the loci chosen as the SWGDAM Y-STR loci. The OSU 10-locus set had a greater average number of alleles per locus and higher average gene diversity than the SWGDAM loci. The OSU 10-locus set found 220 unique haplotypes in 224 individuals. In approximately 6000 pairwise haplotype comparisons for each population with each set of loci, the OSU 10-locus set also yielded a greater average number of allelic differences per pair than the SWGDAM loci. Finally, the overall linkage disequilibrium levels were lower for the OSU 10-locus set in the Caucasian population. In general, the OSU 10-locus set revealed a higher power of discrimination than the SWGDAM set.

Forensic efficiency of microsatellites and single nucleotide polymorphisms on the X chromosome

Polymorphisms located on the X chromosome are being increasingly used in forensic studies. However, they have not been studied as extensively as the autosomal and Y-linked polymorphisms. Therefore, we planned to study the population genetics of two sets of X-linked markers, including short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), and particularly analyze the differences at the microgeographical level. Six X-linked STRs (DXS 9895, DXS 7132, DXS 9898, DXS 6789, GATA 172D05, and DXS 7130) and ten SNPs (rs1229078, rs1544545, rs4442270, rs1874111, rs5968332, rs1166756, rs12849634, rs5932595, rs203648, and rs611711) were studied in two population samples from Cantabria, northern Spain, a mixed coastal population and a relatively isolated small population in the Pas valley. There were statistically significant differences in allelic frequencies of the six STRs studied between both populations. On the other hand, only one out of ten SNPs studied showed between-population differences. Overall Fst values were 0.4-2.9% and 1.8-2.2% for the STRs and the SNPs, respectively. The overall power of discrimination for female samples was higher than 99.99% for both groups of markers. Therefore, these sets of X-linked STRs and SNPs seem to be potentially useful in forensic genetics, but care should be taken when interpreting results from cases that originate from small and relatively isolated populations.

Estimating sex-specific processes in human populations: Are XY-homologous markers an effective tool?

Homologous markers on the sex-specific regions of the X- and Y-chromosomes are differentially inherited through males and females, and have similar molecular characteristics. They may therefore be useful as a complement to the comparison of mtDNA and Y-chromosomal haplotypes for estimating sex-specific processes shaping human population structure. To test this idea, we analyzed XY-homologous microsatellite diversity in 33 human populations from Africa, Asia and Europe. Interpopulation comparisons suggest that the generally discordant pattern of genetic variation observed for X- and Y-linked markers could be an outcome of sex-specific migration processes (m(females)/m(males) approximately 3) or sex-specific demographic processes (N(females)/N(males) approximately 11) or a combination of both. However, intrapopulation diversity estimated by the X/Y ratio Watterson estimator (theta(H(Y))/theta(H(X))) suggests that the scenarios required to explain the global genetic variation of XY-homologous markers are many and complex, and that the sex-specific processes (effective population size and migration rate) shaping human population structures are likely to be specific to each population under study. XY-homologous markers provide an insight into the genuine complexity of sex-specific processes, and their further exploitation in human population studies seems worthwhile.

Gender-specific amplification of Japanese macaque genes using primers for the human DYS391 and DYS438 loci

The species specificity of 10 human Y chromosomal short tandem repeat loci, DYS19, DYS385, DYS389, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439, was examined in the Japanese macaque, Macaca fuscata. Primers for loci DYS391 and DYS438 only yielded an amplification product from male samples. The PCR products amplified with the DYS391 primers showed no inter-individual differences in migration rate in electrophoretic experiments. Sequence analysis revealed that these PCR products consisted of 287 bases containing tandem repeats of TC and TATC. The numbers of TC and the TATC repeats varied between individuals. The TC repeat does not exist in human and chimpanzee sequences. The PCR products amplified by the DYS438 primers provided no evidence of inter-individual variation between the six male Japanese macaque samples. In the Japanese macaque, PCR gives a 184 base pair product, in contrast to human sample from which the products are 203-233 bases in size. The primers for four loci, DYS19, DYS385, DYS389 and DYS437 produced PCR products from both male and female Japanese macaques. The primers for the other loci, DYS390, DYS392, DYS393 and DYS439, did not yield PCR products.

Microsatellite variation and evolutionary history of PCDHX/Y gene pair within the Xq21.3/Yp11.2 hominid-specific homology block

To better understand the evolutionary dynamics of repetitive sequences in human sex chromosomes, we have analyzed seven new X/Y homologous microsatellites located within PCDHX/Y, one of the two recently described gene pairs in the Xq21.3/Yp11.2 hominid-specific homology block, in samples from Portugal and Mozambique. Sharp differences were observed on X/Y allele distributions, concerning both the presence of private alleles and a different modal repeat length for X-linked and Y-linked markers, and this difference was statistically significant. Higher diversity was found in X-linked microsatellites than in their Y chromosome counterparts; when comparing populations, Mozambicans showed more allele diversity for the X chromosome, but the contrary was true for the Y chromosome microsatellites. Evolutionary patterns, relying on intragenic PCDHX/Y SNPs, also revealed distinct scenarios for X and Y chromosomes. Greater microsatellite diversity was displayed by African X chromosomes within the most common haplotypes shared by both populations, whereas higher microsatellite diversity was found in Portugal for the ancestral Y chromosome haplotype. The most frequent PCDHY haplotype in Portuguese was the derived one, and it was not found in Mozambicans. TMRCA estimated by the rho parameter resulted in 13,700 years (7,500-20,000 years), which is consistent with a recent, post-Out-of-Africa origin for this haplotype. In conclusion, the newly described microsatellite loci generally displayed greater X-linked to Y-linked diversity and this pattern was also detected with slower evolving markers, with a remarkable differentiation between populations observed for Y chromosome haplotypes and, thus, greater divergence among Y chromosomes in human populations.

Evolutionary dynamics of duplicated microsatellites shared by sex chromosomes

Segmental duplications on sex chromosomes constitute an important proportion of recent duplications (approximately 30%). Among those, the evolution of duplicated noncoding DNA is still poorly investigated. We focus our work on repeated DNA sequences extensively used in population genetics and evolution: microsatellites. Six duplicated (CA), microsatellite loci, located on the homologous region of human sex chromosomes, were studied at the intraspecific level in Homo sapiens and by an orthologous comparison in eight primate species. At the intraspecific level, we evaluated the congruence in paralogous divergence between the flanking sequences of the six microsatellites and the approximately 2.2-kb surrounding sequences and observed that both phylogenies are congruent. At the interspecific level (8 species of primates: 54 individuals), we analyzed the sequence polymorphism and divergence of each orthologous locus for both the flanking sequence and the microsatellite. The results showed a lower divergence of flanking sequences than expected in noncoding DNA and a relative stability of the first nucleotides close to the microsatellite. The location of each CAIII locus in a Low Copy Repeated element containing duplicated VCX/Y genes (approximately 1 kb) suggested that direct or indirect selection could explain these results. Moreover, the substitution rates in the flanking sequences and in the microsatellites were correlated. Thus, the evolutionary dynamics of microsatellites seems closely linked to the variation of spontaneous mutations in the surrounding regions.

Genetic diversity of Y-specific STRs in chimpanzees (Pan troglodytes)

Using the primers described for humans, sequences for 11 Y-specific microsatellites (DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, GATA A10, A7.1, A7.2, C4, and H4 [Gusmão et al., in press]), previously described in 10 male chimpanzees (Pan troglodytes), were confirmed in nine additional male chimpanzees. Sequences for nine additional microsatellites (DYS19, DYS385I and II, DYS389I and II, DYS390, DYS391, DYS392, and DYS393) were determined in all 19 male chimpanzees; homology to human Y-Short Tandem Repeat (STRs) was confirmed by sequencing. Good amplification results were not obtained for DYS19 and DYS385I/II. Two amplicons were obtained for DYS389I/II, but in contrast to humans, the larger fragment was not Y-specific. Moreover, no polymorphism was observed for DYS434, DYS435, or GATA A10. Consequently, these eight STRs were eliminated from further analyses, and haplotype and allele frequencies were estimated for the remaining 12 STRs. A high haplotype diversity value was found (1.000 +/- 0.017), demonstrating the usefulness and informative power of these Y-STRs for future studies on chimpanzee population genetics.