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Rapid DNA identification is the use of a rugged, field-deployable system to generate short tandem repeat (STR) profiles in law enforcement, military, immigration, and homeland security applications. A performance verification study was conducted on the ANDE Rapid DNA identification system using FlexPlex27, a highly multiplexed, 27 locus assay that generates data for the expanded CODIS core loci and all additional STR loci required for international databasing. The assay contains 23 autosomal loci (D1S1656, D2S1338, D2S441, D3S1358, D5S81, D6S1043, D7S820, D8S1179, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, CSF1PO, Penta E, TH01, vWA, TPOX, and SE33), three Y-chromosomal loci (DYS391, DYS576, and DYS570), and Amelogenin. Study results demonstrate that the instrument is reliable, reproducible, accurate, robust, and ready for a large scale, comprehensive developmental validation by NDIS-participating laboratories. The additional loci in the FlexPlex assay allow for improved STR profile sharing globally, increase the power of discrimination for identification matches, and improve the effectiveness of kinship analyses. Electronic supplementary material The online version of this article (doi:10.1007/s00414-017-1567-9) contains supplementary material, which is available to authorized users.

Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5’ region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA). Fil: Mautner, Martín E.. Biodynamics SRL; Argentina Fil: Perez Santangelo, Agustin. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Torcuato Di Tella; Argentina Fil: Corti Bielsa, Rodrigo M.. Biodynamics SRL; Argentina Fil: Sala, Andrea. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina Fil: Ginart, Santiago. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina Fil: Corach, Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica; Argentina

The scientific community has responded to the misidentification of human cell lines with validated methods to authenticate these cells; however, few assays are available for nonhuman cell line identification. We have developed a multiplex polymerase chain reaction assay that targets nine tetranucleotide short tandem repeat (STR) markers in the mouse genome. Unique profiles were obtained from seventy-two mouse samples that were used to determine the allele distribution for each STR marker. Correlations between allele fragment length and repeat number were determined with DNA Sanger sequencing. Genotypes for L929 and NIH3T3 cell lines were shown to be stable with increasing passage numbers as there were no significant differences in fragment length with samples of low passage when compared to high passage samples. In order to detect cell line contaminants, primers for two human STR markers were incorporated into the multiplex assay to facilitate detection of human and African green monkey DNA. This multiplex assay is the first of its kind to provide a unique STR profile for each individual mouse sample and can be used to authenticate mouse cell lines.

Short tandem repeat (STRs or microsatellites) variants, are highly polymorphic markers that facilitate powerful, high-precision population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic flux. However, STR marker development and analysis by conventional PCR-based methods imposes a workflow bottleneck and is suboptimal for noninvasive sampling strategies such as fecal DNA recovery. While massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery, here we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without requiring a reference genome assembly, and a methodological approach for highly parallel recovery of enriched STR loci. We first employed our approach to design and capture a panel of 5,000 STR loci from a test group of diademed sifakas (Propithecus diadema, n=3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci—97.3-99.6% of STRs characterized with ≥10x non-redundant coverage. Second, we tested our STR capture strategy on a P. diadema fecal DNA preparation, and report robust initial results and methodological suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from regions flanking the STR loci. Our method provides a cost-effective and highly scalable solution for rapid recovery of large STR and SNP datasets in any species without need for a reference genome, and can be used even with suboptimal DNA, which is more easily acquired in conservation and ecological genetic studies.Data DepositionRaw sequencing data are available under Study Accession numbers SRP073167 (genomic shotgun data for Oberon and Tatiana) and SRP076225 (targeted re-sequencing data) from the NCBI Sequence Read Archive. BaitSTR software is available at Github (core BaitSTR programs: https://github.com/aakrosh/BaitSTR; BaitSTR_type.pl companion script for genotyping and block manipulation: https://github.com/lkistler/BaitSTR_type).

Human DNA identification is currently performed by amplifying a small, defined set of short tandem repeat (STR) loci (e.g. CODIS) and analyzing the size of the alleles present at those loci by capillary electrophoresis. High-throughput DNA sequencing (HTS) could enable the simultaneous analysis of many additional STR and single nucleotide polymorphism (SNP) loci, improving accuracy and discrimination. However, it is necessary to demonstrate that HTS can generate accurate data on the CODIS loci to enable backwards compatibility with the FBI NDIS database. Sequencing can also detect novel polymorphisms within alleles that migrate with identical sizes by capillary electrophoresis, improving allele discrimination, and enhancing human identification analysis. All CODIS alleles from an individual can be amplified in a single, multiplex PCR reaction, and combined with additional barcoded samples prior to sequencing. A computational tool for allele identification from multiplexed sequence data has been developed. With longer-read-length platforms, 99.6% allele calling accuracy can be achieved. In the course of STR sequencing protocol development, 12 novel allele sequences have been identified for multiple loci. Sequencing STR loci combined with SNPs will enable new forensic applications.

Short tandem repeat (STR) markers are extensively being used for human identification as well as paternity and forensic case work. X Chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. This study presents development of a new Xchromosomal STR multiplex kit providing short-amplicon (

The analysis of short tandem repeat (STR) markers using polymerase chain reaction (PCR) method has become a widely applied technique in forensic individual identification, rapid detection of chromosome aneuploidies in prenatal and postnatal diagnosis, as well as paternity testing (1-5). Until now, a large number of autosomal and Y-chromosomal markers has been forensically evaluated and used for various purposes. Although X-chromosomal markers have been increasingly applied in both forensic and medical field, their role has not been as extensively investigated as that of autosomal and Y-chromosomal markers. Several investigations have documented the accuracy of fluorescent PCR using STR loci for the rapid prenatal diagnoses of numerical disorders affecting the chromosomes 21, 18, and 13 (6-8). However, the low polymorphism of the most chromosome X and Y markers has hampered the use of the PCR-STR approach for the detection of numerical disorders of sex chromosomes, such as the Turner (45, X) or Klinefelter (47, XXY) syndromes (1,7). A few years ago, a group of authors reported on the application of PCR-STR method in the detection of X-chromosome abnormalities (9,10). One of the biggest challenges is the Turner syndrome, in which a sufficient number of STR loci has to be included to be sure that the individual has only a single X chromosome. The aims of the present study were to investigate the diagnostic informativeness of 5 X-linked STR markers: DXS9895 (Xpter-Xp22.1), GATA172D05 (Xq26.1), DXS6810 (Xq12-Xq21.33), DXS6803 (Xq24-Xq27), and HPRTB (Xq27.3) in the Croatian population and to evaluate the diagnostic value of these 5 loci.

X-chromosome short tandem repeat (STR) polymorphisms are a useful tool in the fields of human population genetics and personal identification and are indispensable in investigating complex kinship or deficiency cases in circumstances where information on mtDNA or Y-chromosome polymorphisms is unavailable. The purpose of this study was to construct a multiplex polymerase chain reaction (PCR) system capable of analyzing a large number of X-STR loci and establish a 16-X-STR database in the Japanese population We developed two octaplex X-STR systems, one including the DXS7424, GATA172D05, HPRTB, DXS8377, GATA31E08, DXS9895, DXS7423, and DXS981 loci and the other the DXS6803, DXS6789, DXS6800, DXS6809, DXS7133, DXS7132, DXS101, and DXS6807 loci, and conducted a population study in 512 Japanese individuals comprising 339 men and 173 women. A 16-locus multiplex system produced unwanted PCR products due to mixture of the DXS9895 primer with the primers of two other loci. However, a 15-locus multiplex system exclusive of the DXS9895 locus did not. The 15-locus multiplex system amplified the largest number of loci among the X-STR multiplex systems used and afforded a power of discrimination of 0.99999999999997 in women and 0.999999997 in men.

Chromosome Y microsatellites seem to be ideal markers to delineate differences between human populations. They are transmitted in uniparental and they are very sensitive for genetic drift. This review will highlight the importance of the Y- Chromosome as a tool for tracing human evolution and describes some details of Y-chromosomal short tandem repeat (STR) analysis. Among them are: microsatellites, amplification using polymerase chain reaction (PCR) of STRs, separation and detection and advantages of X-chromosomal microsatellites. Key words : Forensic, population, review, STR, Y- chromosome.

The aim of this study was of twofold. One was to determine the genetic structure of Iraq population and the second objective of the study was to evaluate the importance of these loci for forensic genetic purposes. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. Twenty (20) STR loci and Amelogenin), including D3S1358, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D2S1338, D5S818, D6S1043, D12S391, D19S433 and Amelogenin amplified by using power plex21® kit. Polymerase chain reaction (PCR) products detected by genetic analyzer 3730xL then data analyzed by PowerStatsV1.2. Based on the allelic frequencies, several statistical parameters of genetic and forensic efficiency have been estimated. This includes the homozygosity and heterozygosity, effective number of alleles (n), the polymorphism information content (PIC), the power of discrimination (DP) and the power of exclusion (PE). The power of discrimination values for all tested loci was from 75 to 96%; therefore, those loci can be safely used to establish a DNA-based database for Iraq population. The high PIC values of the selected markers confirm their usefulness for genetic polymorphism studies and linkage mapping programs in human as well. The mean heterozygosity observed, is expected to have mean PIC values across the 20 loci which were 0.77, 0.81 and 0.78, respectively, indicating high gene diversity. Keywords: Autosomal STR, genetic variation, Iraq, statistical parameters. African Journal of Biotechnology , Vol 13(11), 1210-1218

Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution.

Microsatellites of the X-chromosome have been increasingly studied in recent years as a useful tool in forensic analysis. This review describes some details of X-chromosomal short tandem repeat (STR) analysis. Among them are: microsatellites, amplification using polymerase chain reaction (PCR) of STRs, PCR product evaluation, PCR product purification, separation and detection, data analysis of STR by Identity Software, locus information and allele frequencies for X-chromosomal STR in different populations (DXS101, DXS7423, DXS8377, DXS6789, DXS6807 genetic loci) and advantages of X-chromosomal micro-satellites. In forensic casework and DNA databases, polymorphism in STR is important as a forensic genetic marker. Key words: Short tandem repeat (STR) loci, forensic, interpretation.

Aim To systemically select and evaluate short tandem repeats (STRs) on the chromosome 14 and obtain new STR loci as expanded genotyping markers for forensic application. Methods STRs on the chromosome 14 were filtered from Tandem Repeats Database and further selected based on their positions on the chromosome, repeat patterns of the core sequences, sequence homology of the flanking regions, and suitability of flanking regions in primer design. The STR locus with the highest heterozygosity and polymorphism information content (PIC) was selected for further analysis of genetic polymorphism, forensic parameters, and the core sequence. Results Among 26 STR loci selected as candidates, D14S739 had the highest heterozygosity (0.8691) and PIC (0.8432), and showed no deviation from the Hardy-Weinberg equilibrium. 14 alleles were observed, ranging in size from 21 to 34 tetranucleotide units in the core region of (GATA)9-18 (GACA)7-12 GACG (GACA)2 GATA. Paternity testing showed no mutations. Conclusion D14S739 is a highly informative STR locus and could be a suitable genetic marker for forensic applications in the Han Chinese population.

Short tandem repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of the 1000 Genomes Project. Extensive quality controls show that reliable allelic spectra can be obtained for close to 90% of the STR loci in the genome. We utilize this call set to analyze determinants of STR variation, assess the human reference genome’s representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations., American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship

Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats can alter the function and/or expression of genes allowing organisms to swiftly adapt to novel environments. Importantly, some repeat expansions have also been linked to certain neurodegenerative diseases. Therefore, accurate sequencing of tandem repeats could contribute to our understanding of common phenotypic variability and might uncover missing genetic factors in idiopathic clinical conditions. However, despite long-standing evidence for the functional role of repeats, they are largely ignored because of technical limitations in sequencing, mapping and typing. Here, we report on a novel capture technique and data filtering protocol that allowed simultaneous sequencing of thousands of tandem repeats in the human genomes of a three generation family using GS-FLX-plus Titanium technology. Our results demonstrated that up to 7.6% of tandem repeats in this family (4% in coding sequences) differ from the reference sequence, and identified a de novo variation in the family tree. The method opens new routes to look at this underappreciated type of genetic variability, including the identification of novel disease-related repeats. ispartof: Nucleic Acids Research vol:42 issue:9 pages:5728-5741 ispartof: location:England status: published

Paternity tests are carried out by the analysis of hypervariable short tandem repeat DNA loci. These microsatellite sequences mutate at a higher rate than that of bulk DNA. The occurrence of germline mutations at STR loci posses problems in interpretation of resulting genetic profiles. We recently analyzed 59–159 parent/child allele transfers at 13 microsatellite loci. We identified 12 mutations in 7 microsatellite loci. No mutations were occurred in other 6 loci. The highest mutation rate was observed with 5 mutations at D8S1179 locus at different alleles. The event was always single repeat related. The mutation rate was between 0 and 1.5 x 10-2per locus per gamete per generation. The mutation event is very crucial for forensic DNA testing and accumulation of STR mutation data is extremely important for genetic profile interpretation.

Typing of STR (short tandem repeat) alleles is used in a variety of applications in clinical molecular pathology, including evaluations for maternal cell contamination. Using a commercially available STR typing assay for maternal cell contamination performed in conjunction with prenatal diagnostic testing, we were posed with apparent nonmaternity when the two fetal samples did not demonstrate the expected maternal allele at one locus. By designing primers external to the region amplified by the primers from the commercial assay and by performing direct sequencing of the resulting amplicon, we were able to determine that a guanine to adenine sequence variation led to primer mismatch and allele dropout. This explained the apparent null allele shared between the maternal and fetal samples. Therefore, although rare, allele dropout must be considered whenever unexplained homozygosity at an STR locus is observed.

One multiplex system for the co-amplification of 12 X-chromosomal short tandem repeats (STRs) DXS7132, DXS8378, DXS6809, DXS7133, DXS6789, DXS7424, GATA172D05, HPRTB, DXS7423, GATA31E08, DXS101, DXS6807 and amelogenin was analysed in a sample of 200 (100 males and 100 females) unrelated healthy individuals living in Northern Italy. The χ 2 -test for genotype distribution of the X-chromosomal STRs showed no significant deviation from the Hardy–Weinberg equilibrium (HWE). Allele frequencies between female and male samples were not significantly different in all examined markers. In the kinship cases involving 40 family trios with daughter and 10 father/daughter duos, no mutation was detected. The combined power of discrimination (PDc) of the 12 X-STRs for both females and males was PDc>0.999999.

The analysis of short tandem repeats (STRs) plays an important role in forensic science, human identification, genetic mapping, and disease diagnostics. Traditional STR analysis utilizes gel- or column-based approaches to analyze DNA repeats. Individual STR alleles are separated and distinguished according to fragment length; thus the assay is generally hampered by its low multiplex capacity. However, use of DNA microarray would employ a simple hybridization and detection for field forensics and biology. Here we demonstrate a rapid, highly sensitive method for STR analysis that utilizes DNA microarray technology. We describe two adaptations to accomplish this: the use of competitive hybridization to remove unpaired ssDNA from an array and the use of neural network classification to automate the analysis. The competitive displacement technique mimics the branch migration process that occurs during DNA recombination. Our technique will facilitate the rapid deduction of identity, length, and number of repeats for the multiple STRs in an unknown DNA sample. © 2007 by The National Academy of Sciences of the USA

In forensic casework, Y chromosome short tandem repeat markers (Y-STRs) are often used to identify a male donor DNA profile in the presence of excess quantities of female DNA, such as is found in many sexual assault investigations. Commercially available Y-STR multiplexes incorporating 12–17 loci are currently used in forensic casework (Promega's PowerPlex® Y and Applied Biosystems' AmpFlSTR® Yfiler®). Despite the robustness of these commercial multiplex Y-STR systems and the ability to discriminate two male individuals in most cases, the coincidence match probabilities between unrelated males are modest compared with the standard set of autosomal STR markers. Hence there is still a need to develop new multiplex systems to supplement these for those cases where additional discriminatory power is desired or where there is a coincidental Y-STR match between potential male participants. Over 400 Y-STR loci have been identified on the Y chromosome. While these have the potential to increase the discrimination potential afforded by the commercially available kits, many have not been well characterized. In the present work, 91 loci were tested for their relative ability to increase the discrimination potential of the commonly used ‘core’ Y-STR loci. The result of this extensive evaluation was the development of an ultra high discrimination (UHD) multiplex DNA typing system that allows for the robust co-amplification of 14 non-core Y-STR loci. Population studies with a mixed African American and American Caucasian sample set (n = 572) indicated that the overall discriminatory potential of the UHD multiplex was superior to all commercial kits tested. The combined use of the UHD multiplex and the Applied Biosystems' AmpFlSTR® Yfiler® kit resulted in 100% discrimination of all individuals within the sample set, which presages its potential to maximally augment currently available forensic casework markers. It could also find applications in human evolutionary genetics and genetic genealogy.

Many Y chromosome short tandem repeats (STRs) have been studied and characterized over the past years. A few Y-STRs multiplex kits have been placed on the market for forensic and population study purposes. The aim of our work was to analyse a sample of Sicilian male individuals to evaluate the allelic frequency and, thus, the possibility to implement a genetic database. An 11 loci Y-STR Typing kit was used to yield haplotype profiles from male DNA; amplification products were detected on ABI PRISM 310 Genetic Analyzer and examined by Genemapper v 3.2 (Applied Biosystems). The population sample subjected to the screening resulted to be very different with regards to certain loci whereas for other loci the allelic profile was less variable. Despite a minor discrimination power within the entire population, Y-STRs represent a valid tool to simplify male/female DNA mixture interpretation which is a major challenge when biological traces are found in case of sexual assault.

The samples were collected from unrelated individuals randomly selected from criminal cases. The DNA was extracted from fresh blood leucocytes, bloodstains, tissues, and single hairs by Chelex 100 method (1).

We show the presence of numerous short tandem repeats in the human cytomegalovirus (HCMV) genome and assess their usefulness as molecular markers. The genome is shown to contain at least 24 microsatellite regions that exhibit length polymorphisms. Insertion-deletion polymorphisms at these short tandem repeats are common (80% of repeats examined are polymorphic among two laboratory strains and 10 clinical isolates). This is the first report of widespread microsatellite length polymorphism in a viral genome. Some regions are highly polymorphic: one was revealed by DNA sequencing to contain length variants at five closely linked sites, which combined resulted in 10 variants for this region among the 12 strains and isolates examined. This study not only provides a new molecular marker system for this virus but also extends our understanding of microsatellite polymorphism in two important ways. First, variable-length repeats in HCMV can be considerably shorter than polymorphic repeats previously found in other organisms. Second, highly variable microsatellite repeats are not confined to prokaryotes and eukaryotes, as previously assumed. This variation provides a useful marker system for distinguishing viral isolates, and similar markers are also likely to be found in other large-genome DNA viruses.

A population study in a sample of 211 unrelated individuals from 2 cities in North and Central Italy was carried out to investigate the short tandem repeat (STR) system HUMVWA31. Separation of PCR- amplified DNA fragments was performed by high-resolution horizontal denaturing polyacrylamide gel electrophoresis (PAGE) followed by silver staining. The 7 common alleles were found, together with a new smaller allele. Distribution of the observed genotypes did not deviate from Hardy-Weinberg (H-W) equilibrium. The power of discrimination for this locus was 0.93 and the chance of exclusion was 0.61. Good agreement was found between the allele frequencies in 2 Italian population samples and previous studies on Caucasians. The results of this study suggest that this STR system may be a useful tool in forensic investigations.

International audience; The modifications of hybridization patterns were studied when Southern blots, carrying stallions DNA samples, were probed with eight synthetic tandem repeats (STRs), related by sequence variations in the basic unit. Because STRs preferentially crosshybridize with genomic VNTRs, they usually give patterns looking more like DNA fingerprints, but we found that even small modifications in the STR monomer could cause major changes in the hybridization profiles and could induce a shift of fingerprint pattern towards the detection of only one or two loci. This enables the use of STRs as direct genetic markers for linkage analysis, without cloning of the corresponding DNA fragment. Moreover, the set of STR variants can suggest consensus sequences allowing some prediction of the banding pattern.

International audience; Loci containing tandem repeats of short sequences are sometimes associated with a high level of polymorphism due to variations in the number of repeats. The different variants can be easily characterized by Southern blotting when the repeats span a range from a few hundred bases to a few kilobases, and probes derived from such tandem repeats constitute convenient genetic markers. These structures, usually called minisatellites, are best documented in the human genome, where their number has been estimated to be at least 1500. However, their role and mode of evolution are poorly understood. We are developing tools to evaluate the number of such redundant sequences in a genome and to gain access to new polymorphic loci. Our strategy is based on the use of polymers of oligonucleotides as DNA probes for hybridization on Southern blots. In a previous report, we made polymers with random units of 14 bp and showed that they detect multiple polymorphic loci on human genomic DNA. At present, we are testing the effect of an increase in the complexity of the polymer, as obtained by the use of a longer random unit, and the effect of slight sequence modifications to a particular tandem repeat sequence. In addition, some of these synthetic probes can detect a single polymorphic locus and directly provide new genetic markers.

Background Y chromosomal short tandem repeat (STR) has been used in time estimations for single nucleotide polymorphism (SNP) lineages or eminent persons. But to choose which mutation rate and estimation method in the Y chromosome dating is controversial, since different rates and methods can result in several-fold deviation. Findings We used two deep-rooting pedigrees with full records and reliable dates to directly evaluate the Y chromosomal STR mutation rates and dating methods. We found that the Y chromosomal genealogical mutation rates (OMRB and lmMR) in BATWING method can give the best-fit estimation for historical lineage dating. Conclusions This study validated a very efficient and reliable way for genealogy and historical anthropology researches. Electronic supplementary material The online version of this article (doi:10.1186/s13323-015-0025-z) contains supplementary material, which is available to authorized users.