Autosomal Short Tandem Repeat Research Articles

A Tibetan group from Ngawa Tibetan and Qiang Autonomous Prefecture, southwest China, is rich in genetic polymorphisms at 36 autosomal STR loci and shares a complex genetic structure with other Chinese populations

The Tibetan people are ancient and populous, constituting the seventh-largest of the fifty-five ethnic minority groups in China. The Ngawa Tibetan and Qiang Autonomous Prefecture (NTQAP), situated on the border of northwest and southwest China, has its distinct group relationships. Short tandem repeat (STR) is extremely polymorphic and extensively used in the application of forensic medicine and population genetics. However, it is not clear the genetic information including linkage disequilibrium (LD) by 36 autosomal STR (A-STR) markers in the Tibetan group from NTQAP. The Tibetan population from NTQAP of southwest China was examined for 36 A-STR loci in the research. Every marker across the 36 A-STR loci was consistent with Hardy–Weinberg equilibrium (HWE). The results of the calculation revealed that the total discrimination power (TDP) is 1–2.2552 × 10−42 and the cumulative probability of exclusion (CPE) is 1–1.3031 × 10−16. Subsequently, a total of 345 alleles with allelic frequencies ranging from 0.00382 to 0.55343 were identified, and the allelic numbers varied from 5 in both the TH01 and TPOX markers to 28 in the SE33 locus. The Ngawa Tibetan population, along with other Chinese populations, exhibited influences from historical factors and regional distribution, as indicated by the results of population genetics analysis. We thus first explored the genetic characteristics and correlated forensic parameters of the 36 A-STR markers in NTQAP to fill the gap in the Tibetan population. It was discovered that these 36 autosomal STR markers supplemented forensic STR databases and offered extremely valuable polymorphisms for Chinese forensic applications, such as parentage testing and personal identification. Moreover, the study would contribute additional information regarding the substructure and diversity in the Chinese population.

Processing biological samples from simulated radiological terrorist events using Rapid DNA instruments

Two commercially available portable Rapid DNA instruments were evaluated for their ability to process 1 µL and 10 µL saliva samples deposited on metal and plastic surfaces and contaminated with surrogates of cesium (Cs)-137, strontium (Sr)-90 and cobalt (Co)-60; radioactive materials potentially released during a nuclear weapon accident or a radiological dispersal device detonation. A comparable success rate was noted for both Rapid DNA instruments when considering the number of complete and balanced DNA profiles, the number of profiles with a minimum of 10 autosomal STR loci (out of 23 [FlexPlex™ 27] or 21 [GlobalFiler™ Express]), and the possibility to search a national DNA database in Canada and the United States. Cobalt had an adverse impact on the quality of the megaplex short tandem repeat (STR) DNA profiles derived on each instrument for two of the three contamination levels tested in this study, i.e., 0.05 M and 0.1 M as reflected by a reduced number of detected alleles and decreased profile peak heights. Strontium exhibited some adverse effect on the Rapid DNA results when used at the highest contamination level (0.1 M) whereas cesium had none. No new artifacts were observed in the Rapid DNA profiles of samples spiked with the non-radiogenic surrogates. Importantly, in the context of a radiological/nuclear (RN) event, the ANDE™ 6C offers the possibility to dispose of all radioactive materials associated with contaminated samples quickly using a chip on which all steps of the Rapid DNA process are performed whereas the RapidHIT™ ID accumulates radioactive materials for many days before disposal. An individual handling 25 samples in a week (5 per day) on the RapidHIT™ ID at a 30.5 cm distance with a 5 min exposure to the radioactive source estimated at every run would exceed the 0.042 µSv/5 min limit with gamma dose rates for Cs at 0.13 mSv and for Co at 3.8 mSv. Beta dose rates calculated for the surrogate isotopes at the three concentrations tested were also above the recommended radiation exposure limit of 1 mSv/yr (0.042 µSv/5 min). Various potential mechanisms of action behind the interference noted for Sr and Co at high concentrations are presented. These elements may play a role in the steps prior to PCR (at the DNA molecule by binding to bases or to phosphate groups), during PCR (at the DNA polymerase as cofactors for catalytic sites), or even during amplified DNA fragment detection (as fluorescence quenchers).

Determination of allele frequencies in 15 autosomal short tandem repeat (STR) loci of Arab residents in Iraq

Determination of allele frequencies in 15 autosomal short tandem repeat (STR) loci of Arab residents in Iraq

Internal validation of the GA118-24B Genetic Analyzer, a stable capillary electrophoresis system for forensic DNA identification.

The GA118-24B Genetic Analyzer (hereafter, "GA118-24B") is an independently developed capillary electrophoresis instrument. In the present research, we designed a series of validation experiments to test its performance at detecting DNA fragments compared to the Applied Biosystems 3500 Genetic Analyzer (hereafter, "3500"). Three commercially available autosomal short tandem repeat multiplex kits were used in this validation. The results showed that GA118-24B had acceptable spectral calibration for three kits. The results of accuracy and concordance studies were also satisfactory. GA118-24B showed excellent precision, with a standard deviation of less than 0.1 bp. Sensitivity and mixture studies indicated that GA118-24B could detect low-template DNA and complex mixtures as well as the results generated by 3500 in parallel experiments. Based on the experimental results, we set specific analytical and stochastic thresholds. Besides, GA118-24B showed superiority than 3500 within certain size ranges in the resolution study. Instead of conventional commercial multiplex kits, GA118-24B performed stably on a self-developed eight-dye multiplex system, which were not performed on 3500 Genetic Analyzer. We compared our validation results with those of previous research and found our results to be convincing. Overall, we conclude that GA118-24B is a stable and reliable genetic analyzer for forensic DNA identification.

Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system

BackgroundMassively Parallel Sequencing (MPS) allowed an increased number of information to be retrieved from short tandem repeat (STR) analysis, expanding them not only to the size, as already performed in Capillary Electrophoresis (CE), but also to the sequence. MPS requires constant development and validation of the analytical parameters to ensure that the genotyping results of STRs correspond to those obtained by CE. Given the increased frequency of usage of Y-STRs as supplementary markers to the autosomal STRs analysis, it is urgent to validate the concordance of the typing results between CE and MPS analyses.Methods and resultsDNA extracted from 125 saliva samples of unrelated males was genotyped using Yfiler™ Plus PCR Amplification Kit and ForenSeq™ DNA Signature Prep Kit, which were analyzed by SeqStudio™ Genetic Analyzer for HID and MiSeq™ FGx Forensic Genomics System, respectively. For each shared Y-STR, allele designation, number of length- and sequence-based alleles per locus, stutter percentage, and the intra-locus balance of multicopy Y-STRs were screened.ConclusionsAlthough the number of forensic genetics laboratories that are applying the MPS technique in routine analysis is small and does not allow a global assessment of MPS limitations, this comparative study highlights the ability of MPS to produce reliable profiles despite the generation of large amounts of raw data.

Pinpointing the Short-tandem Repeats Alleles for Ethnic Inferencing in Forensic Identification by K-medoids Approach

Abstract Background: The role of DNA analysis for ethnicity inferencing is a topic that attracts much interest from researchers in forensic identification, especially for identifying unknown bodies and trace evidence. So far, the approaches considered effective for ethnic inferencing are autosomal single-nucleotide polymorphisms, Y-chromosome short-tandem repeats (STRs), and mitochondrial DNA haplotyping, which successfully demonstrates the association of specific nucleotides or patterns with population groups. Ethnic inferencing based on autosomal STRs is complex due to the nature of recombination in gamete formation. Aim: This study attempts to use clustering analysis to associate alleles and loci of autosomal STRs with population groups. Materials and Methods: We examined the allele frequency data from 19 STRs loci from the Malay Indonesian population (n = 470) to compare with other populations, namely, Chinese Indonesian (n = 133) and four reference populations (Malay Malaysian, Filipino, Chinese, and Caucasian). K-Medoids clustering analysis was carried out to pinpoint alleles and loci affecting the population clustering process. Results: The first stage of clustering results placed Malay Indonesians and four other Asian populations, namely, Chinese Indonesian, Malay Malaysian, Filipino, and Chinese, in Cluster 1, whereas the Caucasian group was in Cluster 2. It indicates that the CSF1PO, D5S818, and D8S1179 loci significantly distinguished the five Asian population groups from the Caucasian group, whereas D2S441, D8S1179, and D22S1045 were the three loci that significantly influenced the separation between Malay Indonesians and other groups. Conclusions: We conclude that K-medoids clustering analysis has the potential to play a role in ethnicity estimation by pinpointing specific STRs alleles.

Developmental validation of a novel multiple genotyping assay with 24 Canine STR loci

Canine individual identification and parentage testing are essential in various fields, including forensics and breeding programs. This study aimed to develop and validate the Canine 25 A kit, a multiplex polymerase chain reaction (PCR) system designed to address these critical requirements. This novel system enables the simultaneous amplification of 24 canine autosomal short tandem repeat (STR) loci and one sex-determining marker. Validation of the Canine 25 A kit was conducted following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, demonstrating significant sensitivity, high inhibitor tolerance, canine specificity within a mixture, species specificity, and precision in genotype determination. The Canine 25 A kit was crucial in resolving several forensic cases, such as casework samples from a dog attack incident and parentage determination. Its effectiveness in genotyping these samples highlights its significance in forensic applications. Population genetic parameter analysis revealed a high discriminatory power, as indicated by the calculated combined discrimination power (CDP) values for each breed exceeding 0.999 999 999 999, while the combined power of exclusion (CPE) surpassed 0.9999. Overall, the Canine 25 A kit offers a precise and dependable tool for canine individual identification and parentage determination.

Microsatellites used in forensics are in regions enriched for trait-associated variants

The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are the basis of the vastmajority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS loci are thought to contain little information about ancestry or traits. However, in the past 20 years, a growing field has identified hundreds of thousands of genotype-trait associations. Here, we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. Although this study cannot establish or quantify associations between CODIS genotypes and phenotypes, we find that the regions around the CODIS loci are enriched for both known pathogenic variants (> 90th percentile) and for trait-associated SNPs identified in genome-wide association studies (GWAS) (≥ 95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs.

Separation mixed semen of two individuals using magnetic beads coupled ABH blood group antibody.

In sexual assault cases, one of the most common samples collected is a mixed semen stain, which is often found on the vagina, female underwear, or bed sheets. However, it is usually difficult to identify the perpetrator based on this sample alone. One technique that has been developed to address this issue is magnetic bead-based separation. This method involves using modified magnetic microspheres to capture and enrich specific target cells, in this case, sperm cells. In this study, we utilized magnetic beads coupled with ABH blood group antibody to isolate sperm cells from an individual of a single ABO blood type. Subsequently, polymerase chain reaction amplification and capillary electrophoresis were employed to perform the genotyping the short tandem repeat (STR) loci. This approach allows for the identification of different individuals in a mixed seminal stain sample from two individuals, by first separating sperm cells based on ABH antigen differences and subsequently utilizing autosomal STR typing on the enriched single blood group cells.

Validation of the Microreader™ 36A ID System for forensic genetic casework and database construction

ABSTRACT Autosomal short tandem repeats (STRs) are crucial in identifying humans. Herein, a developmental validation was performed for a newly generated autosomal STR kit (Microreader™ 36A ID System). The sensitivity of this kit was fine when the input DNA dropped down to 0.02 ng/uL. Mixture analysis showed that when male:female = 200 pg: 5400 pg, full profiles of both individuals could be obtained. When inhibited substances existed, all alleles were acquired up to 2000 μM haematin, 1000 ng/μL humic acid or 250 ng/μL tannic acid. The kit exhibited a high precision level with no more than 0.29 nt standard deviation of allele size, with the accuracy (the difference of allele size between the true allele and ladder allele) no more than 0.4 nt. The total discrimination power of this system in the Chinese Han and Hui population was larger than 1–0.1 × 10−30. For the full-sibling test, the identical-by-state (IBS) score varied from 37 to 46, while it was from 21 to 28 when using the AGCU Express marker 22 STR Kit. This kit can increase the autosomal STR information of a single PCR reaction and is promising in the casework of forensic genetic as well as database construction.

Short Tandem Repeat (STR) Profiling of Earwax DNA Obtained from Healthy Volunteers.

The present study aimed to establish human earwax as a potential source of DNA evidence that could be effectively used in human identification. Sixty earwax samples were obtained from 15 healthy male and female Saudi volunteers living in Riyadh, Saudi Arabia. Four consecutive earwax swab samples were obtained from each volunteer and stored for 1, 15, 30 and 60 days. Earwax samples were stored at room temperature (20-22 °C). Reference oral swab was also taken from each volunteer. DNA was extracted by QIAamp DNA Mini kit and quantified by real-time polymerase chain reaction (RT-PCR) on 7500 Thermal Cycler. Autosomal STR loci were amplified using AmpFLSTR™ Identifiler™ Plus PCR Amplification Kit (Thermo Fisher Scientific, Carlsbad, CA, USA). Amplified fragments were size separated and analyzed on a 3500 Genetic Analyzer. Complete autosomal STR profiles were obtained from the earwax swabs of all the volunteers stored up to 30 days after the collection. Some STR profiles were partially obtained 60 days after the earwax collection. Allelic drop-out, allelic drop-in, and stutters were seen in earwax samples analyzed 60 days after the collection. The results have shown that human earwax can be a potential source of DNA evidence for human identification up to 30 days after the earwax collection. It is recommended to quickly analyze earwax samples or store them at room temperature or at -10 °C after their recovery from the crime scene.

Role of Product of Conception and DNA Profiling in Forensic Cases: A Case Study

At this present time, sexual assault on minors has become a major concern in our country. Social unawareness of victims and perpetrators is an emerging issue in sexual assault cases. It has been observed that most of the cases are being reported in the age group of 17–19 years old. Whenever such cases are reported to law enforcement agencies, the victims are brought to hospitals for the termination of pregnancy. In such cases, the product of conception can play a vital and key role in ascertaining paternity. In this present research work, we considered a case in which three different samples were preserved with different preservatives. The extensive problem was to determine the fleshy perceptible as POC because most segments of this material were from mothers. At the present moment, this study concludes that most of the samples provided were not substantive POC. These are part of the placenta and other fleshy material of the mother. Out of three samples, two gave the autosomal STR profile of the victim instead of POC, while one sample was able to conclude the result based on one set of alleles of autosomal STR (Short Tandem Repeat) matching the father. Two of the last samples gave the same STR Y profile to the father.

Pre-analytical Associated Factors of Foreign DNA Detection Beneath Deceased’s Fingernails

Objective: To assess the pre-analytical factors including hand-side, representative collection technique and individual forensic physician for foreign deoxyribonucleic acid (DNA) detection in specimen collected from deceased’s fingernails. Material and Methods: This cross-sectional study, of an initial 164 samples from the fingernails of both hands, of 82 deceased caseworks; from 2010 to 2018, at the Forensic Unit, Faculty of Medicine, Prince of Songkla University. The autosomal short tandem repeats profile fingernail DNA results, pre-analytical factors, and the deceased’s characteristics were obtained from the records. The fingernail DNA outcomes were evaluated and ranked into five groups, i.e., high-level profile, low-level profile, or residual profile; if foreign alleles of more than 11 alleles, 4 to 11 alleles, or less than 4 alleles were detected, respectively. The non-specific profile group consisted of foreign DNA being detected; however the peak signals were below the decisional threshold. The unidentified group consisted of no foreign DNA being detected. The full model underwent both directional stepwise model selection, and the resulting model with the lowest Akaike information criterion was selected as the final model. The final model was analyzed by ordinal logistic regression for significant associated factors: at a 95% confidence level. Results: The representative collection technique is an associated factor, via the use of fingernail swabs (adjusted odds ratio (ORa)=13.44, 95% confidence interval (CI)=2.89–62.45), and had a larger effect size than using fingernail cuttings (ORa=6.84, 95% CI=1.47–31.86). Conclusion: At post-mortem examination, for the collection of foreign DNA from fingernails, the use of fingernail swabs, as a collection technique, is of particular interest.

Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations.

The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.

Developmental validation of the ForenSeq MainstAY kit, MiSeq FGx sequencing system and ForenSeq Universal Analysis Software

For human identification purposes, forensic genetics has primarily relied upon a core set of autosomal (and to a lesser extent Y chromosome) short tandem repeat (STR) markers that are enriched by amplification using the polymerase chain reaction (PCR) that are subsequently separated and detected using capillary electrophoresis (CE). While STR typing conducted in this manner is well-developed and robust, advances in molecular biology that have occurred over the last 15 years, in particular massively parallel sequencing (MPS) [1-7], offer certain advantages as compared to CE-based typing. First and foremost is the high throughput capacity of MPS. Current bench top high throughput sequencers enable larger batteries of markers to be multiplexed and multiple samples to be sequenced simultaneously (e.g., millions to billions of nucleotides can be sequenced in one run). Second, compared to the length-based CE approach, sequencing STRs increases discrimination power, enhances sensitivity of detection, reduces noise due to instrumentation, and improves mixture interpretation [4,8-23]. Third, since detection of STRs is based on sequence and not fluorescence, amplicons can be designed that are shorter in length and of similar lengths among loci, where possible, which can improve amplification efficiency and analysis of degraded samples. Lastly, MPS offers a single format approach that can be applied to analysis of a wide variety of genetic markers of forensic interest (e.g., STRs, mitochondrial DNA, single nucleotide polymorphisms, insertion/deletions). These features make MPS a desirable technology for casework [14,15,24,25-48]. The developmental validation of the ForenSeq MainstAY library preparation kit with the MiSeq FGx Sequencing System and ForenSeq Universal Software is reported here to assist with validation of this MPS system for casework [49]. The results show that the system is sensitive, accurate and precise, specific, and performs well with mixtures and mock case-type samples.

Genetic Population Flows of Southeast Spain Revealed by STR Analysis

The former Kingdom of Granada, comprising the provinces of Granada, Málaga, and Almería (GMA), was once inhabited for over 700 years (711–1492 AD) by a North African population, which influenced its creation and establishment. The genetic data on 15 autosomal short tandem repeats (STRs) in 245 unrelated donor residents were examined in order to assess any possible admixture. As the two surnames in Spain follow an inheritance similar to the Y chromosome, both surnames of all 245 unrelated individuals were queried and annotated. The Spanish Statistics Office website was consulted to determine the regions with the highest frequency of individuals born bearing each surname. Further, several heraldry and lineage pages were examined to determine the historical origin of the surnames. By AMOVA and STRUCTURE analysis, the populations of the three provinces can be treated genetically as a single population. The analysis of allele frequencies and genetic distance demonstrated that the GMA population lay in the Spanish population group but was slightly more similar to the North African populations than the remainder of the Spanish populations. In addition, the surnames of most individuals originated in Northern and Central Spain, whereas most surnames had higher frequencies in Southern Spain. These results confirm that the GMA population shows no characteristics that reflect a greater genetic influence of North African people than the rest of the populations of the Iberian Peninsula. This feature is consistent with the historical data that African inhabitants were expelled or isolated during the repopulation of the region with Spaniards from Northern Spain. The knowledge of present populations and their genetic history is essential for better statistical results in kinship analyses.

Sequence-based allelic variations and frequencies for 22 autosomal STR loci in the Lebanese population

This is the first study that characterizes the sequence-based allelic variations of 22 autosomal Short Tandem Repeat (aSTR) loci in a population dataset collected from Lebanon. Genomic DNA extracts from 195 unrelated Lebanese individuals were amplified with PowerSeq 46GY System Prototype. Targeted amplicons were subjected to DNA library preparation and sequenced on the Verogen MiSeq FGx Sequencing System. Raw FASTQ data files were processed by STRait Razor v3. Sequence strings were annotated according to the considerations of the DNA Commission of the International Society for Forensic Genetics (ISFG) and tabulated herein with their respective allelic frequencies and GeneBank accession and version numbers. The sequenced Lebanese dataset resulted in 429 distinct allelic sequences as compared to the 236 alleles identified by length only. The increase in the number of alleles was observed at 18 out of 22 aSTR loci and was attributed to the sequence variations residing in both the STR repeat motifs and flanking regions. The study uncovered 25 novel aSTR allelic sequences across 12 loci for which GenBank records did not previously exist in the STRSeq BioProject, PRJNA380127. For a concordance check, the length-based allelic calls derived from the full sequences were compared to those genotyped using capillary electrophoresis (CE) methods. Population genetic parameters relevant to the evaluation of forensic DNA evidence were assessed for the sequence-based data and compared to the parameters generated from the length-based information. Using the sequence-based data, Analysis of MOlecular VAriance (AMOVA), genetic distances, and population genetic structure were evaluated for 1231 individuals sampled from the Lebanese and four U.S. populations (African American, Asian, Caucasian, and Hispanic). The results were tabulated and visualized in a population tree, multidimensional scaling scatter plots, and bar plots. This newly established sequence-based database for the Lebanese population can be beneficial for extending NGS applicability to casework or paternity testing and assessing the strength of evidence for NGS-STR profiles. The described novel sequence variants at certain loci can further help in the effort to characterize the sequence diversity of STR markers from different populations around the world.

Genetic investigation of 124 SNPs in a Myanmar population using the Precision ID Identity Panel and the Illumina MiSeq

Single nucleotide polymorphisms (SNPs) have become popular in forensic genetics as an alternative to short tandem repeats (STRs). The Precision ID Identity Panel (Thermo Fisher Scientific), consisting of 90 autosomal SNPs and 34 Y-chromosomal SNPs, enabled human identification studies on global populations through next-generation sequencing (NGS). However, most previous studies on the panel have used the Ion Torrent platform, and there are few reports on the Southeast Asian population. Here, a total of 96 unrelated males from Myanmar (Yangon) were analyzed with the Precision ID Identity Panel on a MiSeq (Illumina) using an in-house TruSeq compatible universal adapter and a custom variant caller, Visual SNP. The sequencing performance evaluated by locus balance and heterozygote balance was comparable to that of the Ion Torrent platform. For 90 autosomal SNPs, the combined match probability (CMP) was 6.994 × 10−34, lower than that of 22 PowerPlex Fusion autosomal STRs (3.130 × 10−26). For 34 Y-SNPs, 14 Y-haplogroups (mostly O2 and O1b) were observed. We found 51 cryptic variations (42 haplotypes) around target SNPs, of which haplotypes corresponding to 33 autosomal SNPs decreased CMP. Interpopulation analysis revealed that the Myanmar population is genetically closer to the East and Southeast Asian populations. In conclusion, the Precision ID Identity Panel can be successfully analyzed on the Illumina MiSeq and provides high discrimination power for human identification in the Myanmar population. This study broadened the accessibility of the NGS-based SNP panel by expanding the available NGS platforms and adopting a robust NGS data analysis tool.

Genetic analysis of allogenic donor cells after successful allo-limbal epithelial transplantation in simple and cultivated limbal epithelial transplantation procedures

This non-comparative cohort study investigated long-term donor cell survival after allogenic simple/cultivated limbal epithelial transplantations (allo-SLET/allo-CLET, respectively) by genetic analysis. Transplanted corneal epithelial cells, which underwent impression cytology and/or corneal-button biopsy, were examined for personal identities of autosomal short-tandem repeats; the percentages of donor cells were calculated based on matching recipient or donor buccal-DNA references. Twelve patients were included; 4 underwent allo-CLET, 8 underwent allo-SLET. Eight patients (67%) had total limbal stem cell deficiency (LSCD). Genetic analysis was performed postoperatively (mean, 55.3 months). Donor cells were detected in 4 of 12 patients (25%), all of whom underwent allo-SLET; 1 patient had a donor genotype and 3 patients had a mixed donor/recipient genotype. The longest time of donor cell detection was 30 months. Seven patients (58%) used systemic immunosuppressives at the time of genetic analysis (mean use, 22.5 months). Allogenic donor cells survived in both procedures for the long term postoperatively, which encourages the long-term use of systemic immunosuppressives. Donor cells may not be the only factor in graft survival, in that most successful cases had a recipient profile. Their presence for a specific time may promote niches for the patients’ own cells to repopulate, especially for partial LSCD.

A genetic Study of the Ghanaian Population Using 15 Autosomal STR Loci.

Autosomal short tandem repeat (STR) population data collected from a well characterized population are needed to correctly assigning the weight of DNA profiles in the courtroom and widely used for ancestral analyses. In this study, allele frequencies for the 15 autosomal short tandem repeat (STR) loci included in the AmpFlSTR® Identifiler® plus kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) were obtained by genotyping 332 unrelated individuals of Ghanaian origin. Statistical tests on STR genotype data showed no significant departure from Hardy-Weinberg equilibrium (HWE). The overall match probability, combined power of exclusion and combined power of discrimination for these loci were 1 in 3.85 × 1017, 0.99999893 and 0.99999998, respectively. Polymorphic information content (PIC) greater than 0.70 was observed for all loci except TH01 and D13S317. These statistical parameters confirm that this combination of loci is valuable for forensic identification and parentage analysis. Our results were also compared with those for 20 other human populations analyzed for the same set of markers. We observed that the Ghanaian population grouped with other African populations in two-dimensional principal coordinate (PCO) and a neighbor-joining (N-J) data mapping and placed closest to Nigerians. This observation reflects cultural similarities and geographical factors, coupled with the long history of migration and trading activities between Ghana and Nigeria. Our report provides what we believe to be the first published autosomal STR data for the general Ghanaian population using 15 loci genotyped using the AmpFlSTR® Identifiler® plus kit methodology. Our data show that the loci tested have sufficient power to be used reliably for DNA profiling in forensic casework and help to elucidate the genetic history of people living in the country.