Short tandem repeats (STRs) are a class of abundant structural or functional elements in the human genome and exhibit a polymorphic nature of repeat length and genetic variation within human populations. Interestingly, STR expansions underlie about 60 neurological disorders. However, \"stutter\" artifacts or noises render it difficult to investigate the pathogenesis of STR expansions. Here, we systematically investigated STR instability in cultured human cells using GC-rich CAG and AT-rich ATTCT tandem repeats as examples. We found that triplicate bidirectional Sanger sequencing with PCR amplification under proper conditions can reliably assess STR length. In addition, we found that next-generation sequencing with paired-end reads bidirectionally covering STR regions can accurately and reliably assay STR length. Finally, we found that STRs are intrinsically unstable in cultured human cell populations and during single-cell cloning. Our data suggest a general method for accurately and reliably assessing STR length and have important implications in investigating pathogenesis of STR expansion diseases.

In recent years, influenced by the legalization of Cannabis sativa in some countries and regions, the number of people who smoke or abuse C. sativa has continuously grown, cases of transnational C. sativa trafficking have also been increasing. Therefore, fast and accurate identification and source tracking of C. sativa have become urgent social needs. In this study, we developed a new 19-plex short tandem repeats (STRs) typing system for C. sativa, which includes 15 autosomal STRs (D02-CANN1, C11-CANN1, 4910, B01-CANN1, E07-CANN1, 9269, B05-CANN1, H06-CANN2, 5159, nH09, CS1, ANUCS 305, 3735, and ANUCS 302 and 9043), two X-chromosome STRs (ANUCS 501 and 1528), one sex-determining marker (DM016, on Y-chromosome), and a quality control marker (DM029, on autosome). The whole polymerase chain reaction (PCR) process could finish within 1 h, making the system suitable for fast detection. The PCR products were detected and separated with an Applied Biosystems 3500XL Genetic Analyser. Developmental validation studies indicated that the 19-plex typing system was accurate, reliable and sensitive, which could also deconvolute mixed C. sativa samples. Specifically, the sensitivity study showed that a full genotyping profile was obtainable with as low as 125 pg of C. sativa DNA. The species specificity study demonstrated that this multiplex has no cross-reactivity with common non C. sativa DNA. In the population study, a total of 162 alleles at 15 autosomal STRs and 14 alleles at two X-chromosome STRs were detected among 85 samples. The efficiency parameters, including the total discrimination power (TDP) and the combined power of exclusion (CPE) of the system, were calculated to exceed 0.999 999 999 999 988 and 0.998 455 889 684 078, respectively, further proving that the system could meet the needs of individual identification. To the extent of the known studies, this is the first study that included the C. sativa sex-determining marker. In conclusion, the developed new 19-plex STR typing system can successfully achieve the purposes of species identification, gender determination, and individual identification, which could be a powerful tool in tracing trade routes of particular drug syndicates or dealers or in linking certain C. sativa to a crime scene.

Rare adrenal choriocarcinoma should be identified as gestational or nongestational choriocarcinoma because of their different treatment and prognosis. A 29-year-old parous women underwent curettage and right-oviduct resection successively due to irregular vaginal bleeding and positive human chorionic gonadotropin (HCG). Postoperative pathological examinations revealed no intrauterine and extrauterine pregnancy. After that, HCG continued to rise. A 7.6×10.3×11.0 cm mass was present in the left adrenal gland with an uneven inner density and a complete capsule by computed tomography (CT). A biopsy was performed on the mass, which showed us choriocarcinoma. Seven cycles of chemotherapy made her complete response and under supervision. Recurrent diagnosis was done after 3 months. The tumor specimen, the patient\'s blood, and her husband\'s blood were drawn for short tandem repeat (STR) analysis using polymerase chain reaction amplification kit. The genotype of the tumor cells was both maternal and patrilineal, which led to the diagnosis of adrenal gestational choriocarcinoma. The patient was scheduled for adrenalectomy and various chemotherapeutic interventions before and after operation. She achieved complete response and was being followed up again. STR analysis first aids in precise classification of this rare adrenal choriocarcinoma. We encourage using the method to analyze choriocarcinoma outside reproductive organs.

Massively parallel sequencing (MPS), or next generation sequencing (NGS), is a promising methodology for the detection of short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) in forensic genetics. Here, the prototype SifaMPS Panel is designed to simultaneously target 87 STRs and 294 SNPs with forensic interest in a single multiplex in conjunction with the TruSeq™ Custom Amplicon workflow and MiSeq FGx™ System. Two in-house python scripts are adopted for the fastq-to-genotype interpretation of MPS data concerning STR and SNP, respectively. In the present study, by sequencing 50 Chinese Hans and many other DNA samples involved in validation studies, system parameters including the depth of coverage (DoC), heterozygote balance (Hb) and sequence coverage ratios (SCRs), as well as different forensic parameters of STRs and SNPs in a population study, were calculated to evaluate the overall performance of this new panel and its practicality in forensic application. In general, except for two STRs (DYS505 and DYS449) and one SNP (rs4288409) that performed poorly, the other 85 STRs and 293 SNPs in our panel had good performance that could strengthen efficiency for human identification and paternity testing. In addition, discordant STR genotype results between those generated from capillary electrophoresis (CE) and from the MPS platform were clearly illustrated, and these results could be a useful reference for applying these particular non-CODIS STRs in forensic practice.

A growing number of studies have shown immunotherapy to be a promising treatment strategy for several types of cancer. Short tandem repeats (STRs) have been proven to be alternative markers for the evaluation of hypermutability in gastrointestinal (GI) cancers. However, the status of STRs and microsatellite instability (MSI) in other tumors have not yet been investigated. To further compare STR and MSI alterations in different tumors, a total of 407 paired DNAs were analyzed from the following eight tumor types: breast cancer (BC), hepatocellular cancer (HCC), pancreatic cancer (PC), colorectal cancer (CRC), gastric cancer (GC), lung cancer (LC), esophageal cancer (EC), and renal cell cancer (RCC). The STR alteration frequencies varied in different tumors as expected. Interestingly, none of the patients possessed MSI-low (MSI-L) or MSI-high (MSI-H), except for the GI patients. The highest STR alteration was detected in EC (77.78%), followed by CRC (69.77%), HCC (63.33%), GC (54.55%), LC (48.00%), RCC (40.91%), BC (36.11%), and PC (25.71%). The potential cutoff for hypermutability was predicted using the published objective response rate (ORR), and the cutoff of LC and HCC was the same as that of GI cancers (26.32%). The cutoffs of 31.58% and 10.53% should be selected for BC and RCC, respectively. In summary, we compared MSI and STR status in eight tumor types, and predicted the potential threshold for hypermutability of BC, HCC, CRC, GC, LC, EC, and RCC.

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 (CPEduos) and in trios (CPEtrios) 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.

The Blang is a minority living in the mountainous areas of Xishuangbanna Dai Autonomous Prefecture, and they also scatter in the neighboring cities of Lincang and Simao. This population is investigated in this study through PowerPlex® 21 System. The frequency distribution of allele, forensic, and population parameters of 20 autosomal short tandem repeat loci were evaluated based on 207 non-related individuals from Blang minority; meanwhile, the genetic relationships between Blang and 11 related populations were also assessed.

With the continuous development of massively parallel sequencing (MPS), increasing numbers of laboratories have utilized this method for forensic genomic analyses. When sequencing common short tandem repeats (STRs), MPS does have many advantages over the length-based genotyping method that uses traditional capillary electrophoresis (CE) technology. The Precision ID GlobalFiler™ NGS STR Panel v2 was recently released to simultaneously target 31 autosomal STRs (20 expanded Combined DNA Index System (CODIS) core loci and 11 non-CODIS loci) and 4 gender determination loci (Amelogenin, DYS391, SRY and Y-indel (rs2032678)) with the Ion S5™ System. In the current study, we performed a preliminary validation for this novel MPS-STR panel that included the following analyses: repeatability, concordance, stutter and balance, sensitivity, case-type sample testing, stability, mixture and a population investigation. Complete and reliable profiles were obtained using 125 pg of positive control DNA. The commonly encountered types of case samples and artificial mixtures with ratios of 1:1, 1:3 and 3:1 were also fully genotyped. Additional allele sequence variations were detected in samples from 50 unrelated individuals, and subsequently, an increased power of discrimination and power of exclusion were achieved. However, the average depth of coverage (DoC) of the Penta D locus was detected to be dramatically lower than those of other loci, which caused an interlocus imbalance; this could be one of the reasons for the intralocus imbalance of this locus and the 0.18% inconsistent results in the concordance study. Although certain flaws were observed, the informative metrics, including the DoC, sequence coverage ratios (SCRs) and heterozygote balance (Hb), of the novel MPS multiplex in our study were sufficient for reliable sequencing results that were 99.61% in concordance with the capillary electrophoresis (CE) results. In general, the Precision ID GlobalFiler™ NGS STR Panel v2 was demonstrated to be sensitive, reliable and robust and could be a powerful tool for human identification and kinship analyses. Additionally, we look forward to its updated version.

Background: Short tandem repeats (STRs) are powerful genetic markers widely used in human genetics. Population data and locus-specific mutation rates of STRs are crucial for the evaluation and interpretation of genetic evidence in forensic and population genetics.Aim: To investigate the mutation rates of 21 autosomal STRs in a population from central south China.Subjects and methods: This study analysed 3420 paternity cases with a Combined Paternity Index >10,000 from Han population in Hunan. A total of 68,743 meiotic transfers were analysed and 62 mutations were identified.Results: The overall mutation rate of STR loci was 0.9 × 10-3 (95% CI, 0.0007-0.0011) and the locus-specific mutation rates were estimated ranging from 0.0000-0.0023. Locus D1S1656 exhibited the highest mutation rate of 2.3 × 10-3 (95% CI, 0.0005-0.0006), followed by D12S391 with a mutation rate of 2.0 × 10-3 (95% CI, 0.0007-0.0044). No mutation was observed at TPOX, D2S1338 or Penta D. One-step mutation cases accounted for 96.77% of total mutations and the ratio of paternal vs maternal mutations was ∼4.85:1. Inter-population comparisons of locus-specific mutation rates of several STRs revealed significant differences between Han in Hunan and Han in other regions of China. Conclusion: The data justified the use of geographical data in further genetic applications.

The Lisu is an ethnic minority living in highlands or mountain valleys in the northern region of the Indo-China Peninsula. The paper presents the frequency distribution of allele and statistical genetic parameters of forensic relevance for 15 autosomal STR loci found in the AmpFℓSTR® Identifiler® PCR Amplification Kit among a population sample constituted by 1854 non-related Lisu minority individuals residing in the southwestern region of China. The genetic relationships between Lisu population and 14 related populations were assessed.