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The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.
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Genética de Población , Repeticiones de Microsatélite , Masculino , Humanos , Haplotipos , Irán , Cromosomas Humanos Y/genética , ChinaRESUMEN
INTRODUCTION: Iran, a country in the Middle East, has several ethnic and ethno-religious groups and needs its own ethnic-specific databases for the forensic statistical parameters and allele frequency of STR markers. METHODS: We have investigated 600 unrelated Turk individuals from four northwestern provinces of Iran using the Identifiler™ system (TPOX, FGA, vWA, TH01, CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, and D21S11). Furthermore, STR allelic frequencies were compared to previously population-based data. RESULTS AND CONCLUSION: After Bonferroni correction, deviation from Hardy-Weinberg equilibrium (HWE) was observed in the FGA, TPOX, VWA, and D19S433 loci (P value < 0.05). The combined power of discrimination (CPD) and exclusion (CPE) values for all 15 STR loci were 0.9999999999999999999984 and 0.9999999, respectively. In comparison with Azerbaijani and Turkish populations, there were no significant differences on all STR markers. However, in the Chinese Han population, differences at 13 STR loci were detected. Additionally, comparisons of Fischer genetic distance indices (FST) P-values did not reveal any statistically significant difference between Northwestern Iran, Azerbaijan and Iran (Fars) populations. PCA and PCoA analyses showed that our population was grouped with different populations in different quarters, showing a positive and negative correlation, respectively. In the NJ and UPGMA phylogenetic trees, Iranian populations were grouped together. These results demonstrated that the given set of STR markers can be confidently used for all identification tests in Northwestern Iran.
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Agglomerative hierarchical clustering has become a common tool for the analysis and visualization of data, thus being present in a large amount of scientific research and predating all areas of bioinformatics and computational biology. In this work, we focus on a critical problem, the nonuniqueness of the clustering when there are tied distances, for which several solutions exist but are not implemented in most hierarchical clustering packages. We analyze the magnitude of this problem in one particular setting: the clustering of microsatellite markers using the Unweighted Pair-Group Method with Arithmetic Mean. To do so, we have calculated the fraction of publications at the Scopus database in which more than one hierarchical clustering is possible, showing that about 46% of the articles are affected. Additionally, to show the problem from a practical point of view, we selected two opposite examples of articles that have multiple solutions: one with two possible dendrograms, and the other with more than 2.5 million different possible hierarchical clusterings.
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Biología Computacional , Repeticiones de Microsatélite , Análisis por ConglomeradosRESUMEN
Devices of nanopore sequencing can be highly portable and of low cost. Thus, nanopore sequencing is promising in in-field forensic applications. Previous investigations have demonstrated that nanopore sequencing is feasible for genotyping forensic short tandem repeats (STRs) by using sequencers of Oxford Nanopore Technologies. Recently, Qitan Technology launched a new portable nanopore sequencer and became the second supplier in the world. Here, for the first time, we assess the QNome (QNome-3841) for its accuracy in nanopore sequencing of STRs and compare with MinION (MinION Mk1B). We profile 54 STRs of 21 unrelated individuals and 2800M standard DNA. The overall accuracy for diploid STRs and haploid STRs were 53.5% (378 of 706) and 82.7% (134 of 162), respectively, by using QNome. The accuracies were remarkably lower than those of MinION (diploid STRs, 84.5%; haploid, 90.7%), with a similar amount of sequencing data and identical bioinformatics analysis. Although it was not reliable for diploid STRs typing by using QNome, the haploid STRs were consistently correctly typed. The majority of errors (58.8%) in QNome-based STR typing were one-repeat deviations of repeat units in the error from true allele, related with homopolymers in repeats of STRs.
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The identification of human remains is of utmost importance in a variety of scenarios. One of the primary identification methods is DNA. DNA extraction from human remains could be difficult, particularly in situations where the remains have been exposed to environmental conditions and other insults. Several studies tried to improve extraction by applying different approaches. ForensicGEM Universal (MicroGem) is a single-tube approach to DNA extraction and a temperature-driven method that could have some advantages with respect to previous techniques, among them, reducing the risk of contamination, not requiring specialized equipment, or several steps to perform. The aim of this study was to assess, for the first time, the efficiency of DNA extraction and quality of STR profiles applying the MicroGem protocol and modifications of this protocol from tooth samples in comparison with automatic extraction (AE). Our results indicated that AE and MicroGem performed similar, though with variability depending on the MicroGem modifications, increasing the DNA yield and STR profile quality when DNA is concentrated with Microcon. These findings demonstrated the efficiency of this methodology for DNA extraction from human remains while also providing a simple and quick technique suitable to apply in a variety of forensic scenarios.
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Dermatoglifia del ADN , ADN , Repeticiones de Microsatélite , Temperatura , Humanos , ADN/aislamiento & purificación , ADN/análisis , Dermatoglifia del ADN/métodos , Restos Mortales/química , Diente/química , Genética Forense/métodos , Reacción en Cadena de la Polimerasa/métodosRESUMEN
AIMS: While epithelioid trophoblastic tumour (ETT) primarily arises from the uterus, cases have been increasingly documented at extrauterine sites, originating from an ectopic gestation or presenting as a metastatic tumour, leading to the major differential diagnosis of somatic carcinoma with trophoblastic differentiation. The precise separation of a gestational trophoblastic tumour from its somatic carcinoma mimics is highly relevant and crucial for patient management and prognosis. METHODS AND RESULTS: We summarise the clinicopathological and molecular features of four challenging epithelioid malignancies presenting at extrauterine sites, with ETT as the main differential diagnosis. All four tumours demonstrated histological and immunohistochemical features overlapping between a somatic carcinoma and an ETT, combined with inconclusive clinical and imaging findings. Serum beta-hCG elevation was documented in two cases. Short tandem repeat (STR) genotyping was performed and was informative in all cases. The presence of a unique paternal allelic pattern in the tumour tissue confirmed the diagnosis of ETT in two cases with an initial consideration of either somatic carcinoma or suspicion of a gestational trophoblastic tumour. The presence of matching genetic profile with the patient's paired normal tissue was seen in two other cases (both initially considered as ETT), confirming their somatic origin, including one metastatic triple-negative breast carcinoma and one primary lung carcinoma. CONCLUSIONS: Diagnostic separation of ETT at an extrauterine site from its somatic carcinoma mimics can be difficult at the histological and immunohistochemical levels. STR genotyping offers a robust ancillary tool that precisely separates ETT from somatic carcinomas with trophoblastic differentiation.
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Carcinoma , Enfermedad Trofoblástica Gestacional , Neoplasias Uterinas , Embarazo , Femenino , Humanos , Genotipo , Enfermedad Trofoblástica Gestacional/diagnóstico , Enfermedad Trofoblástica Gestacional/genética , Enfermedad Trofoblástica Gestacional/patología , Carcinoma/genética , Útero/patología , Repeticiones de Microsatélite , Neoplasias Uterinas/diagnóstico , Neoplasias Uterinas/genética , Neoplasias Uterinas/patologíaRESUMEN
After hematopoietic stem cell transplantation, chimerism assay is a useful approach to monitor the success of the transplant and to select the appropriate treatment strategy, such as donor leukocyte infusion or immunosuppressive drug dosage. Short tandem repeat PCR is the method that has been accepted as the gold standard for chimerism. However, it has not yet been sufficient to detect mixed chimerism in patients with minimal residual disease. Simultaneously, recent years have been marked by developing sensitive, high-throughput, and accurate molecular genetic assays. These novel methods have subsequently been adapted for the analysis of post-transplant chimerism. In this review, we discuss the technical features of both novel and conventional gold standard chimerism assays. We also discuss their advantages and disadvantages.
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Quimerismo , Trasplante de Células Madre Hematopoyéticas , Humanos , Recurrencia Local de Neoplasia/genética , Trasplante Homólogo , Repeticiones de Microsatélite , Quimera por Trasplante/genéticaRESUMEN
DNA mixture analysis poses a significant challenge in forensic genetics, particularly when dealing with degraded and trace amount DNA samples. Multi-SNPs (MNPs) are genetic markers similar to microhaplotypes but with smaller molecular sizes (< 75 bp), making them theoretically more suitable for analyzing degraded and trace amount samples. In this case report, we investigated a cold case involving a campstool stored for over a decade, aiming to detect and locate the suspect's DNA. We employed both conventional capillary electrophoresis-based short tandem repeat (CE-STR) analysis and next-generation sequencing-based multi-SNP (NGS-MNP) analysis. The typing results and deconvolution of the mixed CE-STR profiles were inconclusive regarding the presence of the suspect's DNA in the mixed samples. However, through NGS-MNP analysis and presence probability calculations, we determined that the suspect's DNA was present in the samples from Sect. 4-1 with a probability of 1-8.41 × 10- 6 (99.999159%). This evidence contradicted the suspect's statement and aided in resolving the case. Our findings demonstrate the significant potential of MNP analysis for examining degraded and trace amount DNA mixtures in forensic investigations.
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Commercial short tandem repeat (STR) kits exclusively contain human-specific primers; however, various non-human organisms with high homology to the STR kit's primer sequences can cause cross-reactivity. Owing to the proprietary nature of the primers in STR kits, the origins and sequences of most non-specific peaks (NSPs) remain unclear. Such NSPs can complicate data interpretation between the casework and reference samples; thus, we developed "NSPlex", an efficient method to discover the biological origins of NSPs. We used leftover STR kit amplicons after capillary electrophoresis and performed advanced bioinformatics analyses using next-generation sequencing followed by BLAST nucleotide searches. Using our method, we could successfully identify NSP generated from PCR amplicons of a sample mixture of human DNA and DNA extracted from matcha powder (finely ground powder of green tea leaves and previously known as a potential source of NSP). Our results showed our method is efficient for NSP analysis without the need for the primer information as in commercial STR kits.
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Dermatoglifia del ADN , Cartilla de ADN , Electroforesis Capilar , Secuenciación de Nucleótidos de Alto Rendimiento , Repeticiones de Microsatélite , Reacción en Cadena de la Polimerasa , Humanos , Dermatoglifia del ADN/métodosRESUMEN
After in vitro fertilization with a single embryo, the parents learned about being pregnant with twins in the 10th week with various indications that an embryonic mix-up could have taken place. The affected couple thus expressed the urgent desire for a clarification of parenthood considering an abortion. However, the prenatal test results would not have been available until the 14/15th week of pregnancy. Legally, then, severe physical or mental distress of the pregnant woman must be claimed by physicians to justify an abortion after the twelfth week. However, a lack of genetic relatedness could lead to serious psychological distress for the parents, making a pregnancy termination possible even after the twelfth week, which is discussed in this case study alongside the interdisciplinary team's ethical, legal, and medical considerations.For the invasive relationship testing, cultivated chorionic villi samples (CVS) from both unborn and saliva samples from the putative parents were genetically analyzed using classical short tandem repeats (STR) analysis. The perfect match of both CVS profiles suggested the occurrence of an unusual late twin shaft, for which, fortunately, parenthood could be confirmed. To our knowledge, this is the first report on a prenatal investigation of a suspected embryo mix-up after assisted reproductive technology (ART), in which parenthood should be fixed. We want to draw attention to this unthinkable scenario, which may increase in the future with ART-induced rising multiple pregnancies.
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Fertilización In Vitro , Humanos , Embarazo , Femenino , Adulto , Repeticiones de Microsatélite , Embarazo Gemelar , Muestra de la Vellosidad Coriónica , Masculino , GemelosRESUMEN
BACKGROUND: The mutational status of ovarian cancer cell line IGROV-1 is inconsistent across the literature, suggestive of multiple clonal populations of the cell line. IGROV-1 has previously been categorised as an inappropriate model for high-grade serous ovarian cancer. METHODS: IGROV-1 cells were obtained from the Netherlands Cancer Institute (IGROV-1-NKI) and the MD Anderson Cancer Centre (IGROV-1-MDA). Cell lines were STR fingerprinted and had their chromosomal copy number analysed and BRCA1/2 genes sequenced. Mutation status of ovarian cancer-related genes were extracted from the literature. RESULTS: The IGROV-1-NKI cell line has a tetraploid chromosomal profile. In contrast, the IGROV-1-MDA cell line has pseudo-normal chromosomes. The IGROV-1-NKI and IGROV-MDA are both STR matches (80.7% and 84.6%) to the original IGROV-1 cells isolated in 1985. However, IGROV-1-NKI and IGROV-1-MDA are not an STR match to each other (78.1%) indicating genetic drift. The BRCA1 and BRCA2 gene sequences are 100% identical between IGROV-1-MDA and IGROV-1-NKI, including a BRCA1 heterozygous deleterious mutation. The IGROV-1-MDA cells are more resistant to cisplatin and olaparib than IGROV-1-NKI. IGROV-1 has a mutational profile consistent with both Type I (PTEN, PIK3CA and ARID1A) and Type II ovarian cancer (BRCA1, TP53) and is likely to be a Type II high-grade serous carcinoma of the SET (Solid, pseudo-Endometroid and Transitional cell carcinoma-like morphology) subtype. CONCLUSIONS: Routine testing of chromosomal copy number as well as the mutational status of ovarian cancer related genes should become the new standard alongside STR fingerprinting to ensure that ovarian cancer cell lines are appropriate models.
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Mutación , Neoplasias Ováricas , Femenino , Neoplasias Ováricas/genética , Neoplasias Ováricas/patología , Humanos , Línea Celular Tumoral , Mutación/genética , Variaciones en el Número de Copia de ADN/genética , Proteína BRCA1/genética , Proteína BRCA2/genética , Dosificación de GenRESUMEN
Pineal lesions represent less than 1% of all brain tumors (Villani et al., Clin Neurol Neurosurg 109:1-6, 2007). The abysmal location and critical neurovascular structures remain a surgical challenge, despite the advent of microneurosurgery. The classical wide surgical suboccipital craniotomy with the supracerebellar infratentorial approach, described by Sir Victor Horsley (Victor, Proc R Soc Med 3:77-78, 1910), is infamous for its considerable surgical morbidity and mortality. This was later upgraded microneurosurgically by Stein to improve surgical outcomes (Stein, J Neurosurg 35:197-202, 1971).Ruge et al. reported the first purely endoscopic fenestration of quadrigeminal arachnoid cysts via this corridor (Ruge et al., Neurosurgery 38:830-7, 1996). A cadaver-based anatomical study by Cardia et al. demonstrated the viability for endoscope-assisted techniques (Cardia et al., J Neurosurg 2006;104(6 Suppl):409-14). However, the first purely endoscopic supracerebellar infratentorial (eSCIT) approach to a pineal cyst was performed in 2008 by Gore et al. (Gore PA et al., Neurosurgery 62:108-9, 2008).Unlike transventricular endoscopy, eSCIT approach poses no mechanical risk to the fornices and can be utilized irrespective of ventricular size. More vascular control and resultant reduction in uncontrolled hemorrhage improve the feasibility of attaining complete resection, especially around corners (Zaidi et al,, World Neurosurg 84, 2015). Gravity-dependent positioning and cerebrospinal fluid (CSF) diversion aid cerebellar relaxation, creating the ideal anatomical pathway. Also, angle of the straight sinus, tentorium, and tectal adherence can often influence the choice of approach; thus direct endoscopic visualization not only counteracts access to the engorged Galenic complex but also encourages sharp dissection of the arachnoid (Cardia et al., J Neurosurg 104:409-14, 2006). These tactics help provide excellent illumination with magnification, making it less fatiguing for the surgeon (Broggi et al., Neurosurgery 67:159-65, 2010).The purely endoscopic approach thwarts the dreaded risk of air embolisms, via simple copious irrigation from a small burr hole (Shahinian and Ra, J Neurol Surg B Skull Base 74:114-7, 2013). The tiny opening and closure are rapid to create, and the smaller wound decreases postoperative pain and morbidity. Recent literature supports its numerous advantages and favorable outcomes, making it a tough contender to traditional open methods.
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Glándula Pineal , Niño , Humanos , Neoplasias Encefálicas/cirugía , Cerebelo/cirugía , Endoscopía/métodos , Neuroendoscopía/métodos , Procedimientos Neuroquirúrgicos/métodos , Glándula Pineal/cirugía , Pinealoma/cirugíaRESUMEN
PURPOSE: To present the developed preimplantation genetic testing (PGT) for spinocerebellar ataxia type 1 (SCA1) and the outcomes of IVF with PGT. METHODS: PGT was performed for two unrelated couples from the Republic of Sakha (Yakutia) with the risk of SCA1 in one spouse. We have developed a system for PGT of a monogenic disease (PGT-M) for SCA1, which includes the analysis of a panel of 11 polymorphic STR markers linked to the ATXN1 gene and a pathogenic variant of the ATXN1 gene using nested PCR and fragment analysis. IVF/ICSI programs were performed according to standard protocols. Multiple displacement amplification (MDA) was used for whole genome amplification (WGA) and array comparative genomic hybridization (aCGH) for aneuploidy testing (PGT-A). RESULTS: Eight STRs were informative for the first couple and ten for the second. Similarity of the haplotypes carrying pathogenic variants of the ATXN1 gene was noted. In the first case, during IVF/ICSI-PGT, three embryos reached the blastocyst stage and were biopsied. One embryo was diagnosed as normal by maternal STR haplotype and the ATXN1 allele. PGT-A revealed euploidy. The embryo transfer resulted in a singleton pregnancy, and a healthy boy was born. Postnatal diagnosis confirmed normal ATXN1. In the second case, two blastocysts were biopsied. Both were diagnosed as normal by PGT-M, but PGT-A revealed aneuploidy. CONCLUSION: Birth of a healthy child after PGT for SCA1 was the first case of successful preimplantation prevention of SCA1 for the Yakut couple and the first case of successful PGT for SCA1 in Russia.
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Ataxina-1 , Repeticiones de Microsatélite , Diagnóstico Preimplantación , Ataxias Espinocerebelosas , Humanos , Ataxias Espinocerebelosas/genética , Ataxias Espinocerebelosas/patología , Ataxias Espinocerebelosas/diagnóstico , Femenino , Ataxina-1/genética , Masculino , Adulto , Embarazo , Repeticiones de Microsatélite/genética , Pruebas Genéticas , Hibridación Genómica Comparativa , Aneuploidia , Fertilización In Vitro , Transferencia de EmbriónRESUMEN
BACKGROUND: The haplotypes from Northern, Southern, Eastern, and Western Kazakhstan, analysed for 27 Y-STR loci, have been contributed to the Y-Chromosome STR Haplotype Reference Database, while the genetic profile of Central Kazakhstan remains inadequately explored. AIM: To investigate the genetic diversity of 27 Y-STR loci in the Kazakh populations from Central Kazakhstan. SUBJECTS AND METHODS: A total of 112 unrelated Central Kazakh males were genotyped via the Yfiler Plus kit. Data analysis yielded haplotype and allele frequencies, and forensic parameters. Genetic distances were graphically represented by a multidimensional scaling plot, with genetic linkages further elucidated through Nei's distance dendrograms and Median-joining networks. RESULTS: A total of 102 haplotypes were detected, of which 96 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.91, respectively. Central Kazakhstan displays a unique cluster in analyses, underscoring its distinct Y-chromosome diversity compared to other Kazakh regions. The analysis of the Naiman tribe, predominantly residing in Central, Southern and Eastern Kazakhstan, revealed three genetic clusters of distinct haplogroups associated with their clans. CONCLUSIONS: The identified haplotypes will enhance the existing reference database for Y-chromosomal studies in Kazakhstan, offering a robust tool for future research in population genetics, forensic science and genetic genealogy.
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Cromosomas Humanos Y , Haplotipos , Repeticiones de Microsatélite , Polimorfismo Genético , Humanos , Kazajstán , Cromosomas Humanos Y/genética , Masculino , Frecuencia de los GenesRESUMEN
BACKGROUND: At present, there are no available genetic data on the AGCU EX22 Kit from the Wuhu Han population. AIM: This study investigates the applicability of the AGCU EX22 kit, designed for the Chinese population for forensic analysis and population genetics of the Wuhu Han population. SUBJECTS AND METHODS: Bloodstains from 1565 unrelated healthy individuals in Wuhu city, Anhui Province, were collected for analysis. The AGCU EX22 kit was used for amplification, and capillary electrophoresis was used to separate the amplification products. Allele frequencies and forensic parameters were determined. The Wuhu Han population was compared to 10 reference populations through genetic distance, a phylogenetic neighbor-joining tree and principal component analysis. RESULTS: In total, 281 alleles and 1187 genotypes were observed. No significant deviations from Hardy-Weinberg equilibrium at any locus were found after Bonferroni's correction. The 21 autosomal short tandem repeat (STR) genetic markers exhibited high informativeness and polymorphism. The cumulative power of discrimination and power of exclusion were 0.999999999999999999999999913380 and 0.999999996752339, respectively. Population comparisons revealed a genetic affinity between Wuhu Han and southern Han populations, except for the Guangdong Han population, which aligned with the traditional geographical division in China. CONCLUSION: The AGCU EX22 Kit, containing 21 STR loci, is suitable for forensic application and population genetics studies in the Wuhu Han population.
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Pueblos del Este de Asia , Repeticiones de Microsatélite , Humanos , Alelos , China , Pueblos del Este de Asia/genética , Genética Forense , Frecuencia de los Genes , Genética de Población , Voluntarios Sanos , Filogenia , SangreRESUMEN
DNA analysis plays a crucial role in forensic investigations, helping in criminal cases, missing persons inquiries, and archaeological research. This study focuses on the DNA concentration in different skeletal elements to improve human identification efforts. Ten cases of unidentified skeletal remains brought to the Institute of Forensic Medicine in Timisoara, Romania, underwent DNA analysis between 2019 and 2023. The results showed that teeth are the best source for DNA extraction as they contain the highest concentration of genetic material, at 3.68 ng/µL, compared to the petrous temporal bone (0.936 ng/µL) and femur bone (0.633 ng/µL). These findings highlight the significance of teeth in forensic contexts due to their abundant genetic material. Combining anthropological examination with DNA analysis enhances the understanding and precision of identifying human skeletal remains, thus advancing forensic science. Selecting specific skeletal elements, such as the cochlea or teeth, emerges as crucial for reliable genetic analyses, emphasizing the importance of careful consideration in forensic identification procedures. Our study concludes that automated DNA extraction protocols without liquid nitrogen represent a significant advancement in DNA extraction technology, providing a faster, more efficient, and less labor-intensive method for extracting high-quality DNA from damaged bone and tooth samples.
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ADN , Diente , Humanos , Diente/química , ADN/aislamiento & purificación , ADN/genética , Huesos/química , Restos Mortales/química , Genética Forense/métodos , Masculino , Rumanía , FemeninoRESUMEN
Body fluid identification plays a crucial role in criminal investigations. Because of their presence in many cases, blood and semen are the most relevant body fluids in forensic sciences. Based on antigen-antibody reactions binding unique proteins for each body fluid, serological assays represent one of the most rapid and highly specific tests for blood and semen. Currently, few studies have assessed the factors affecting body fluid identification by applying these assays. This work aimed to study the effect of different fabrics from clothes and time since deposition on identification through immunochromatographic tests for blood and semen, DNA isolation, and STR profiling from these samples. Body fluids were deposited on black- and white-dyed denim and cotton fabrics, and on leather. Afterward, blood and semen were sampled at 1 day, 30 days, and 90 days after deposition and identified by using the SERATEC® HemDirect Hemoglobin Test and the PSA Semiquant and SERATEC® BLOOD CS and SEMEN CS tests, respectively. Laboratory and crime scene tests presented similar performances for the detection of blood and semen stains on every tested fabric. No differences were found on band intensities between timepoints for all fabrics. It was possible to recover and identify blood and semen samples up to three months after deposition and to obtain full STR profiles from all the tested fabrics. Both body fluid STR profiles showed differences in their quality between 1 and 90 days after deposition for all fabrics except for black cotton for semen samples. Future research will expand the results, assessing body fluid identification on other substrates and under different environmental conditions.
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Líquidos Corporales , Semillas , Humanos , Semillas/química , Líquidos Corporales/química , Secreciones Corporales/química , Análisis de Semen , ADN/análisis , Saliva/química , Dermatoglifia del ADNRESUMEN
There may be cases where malignant tumor samples can be used for forensic DNA profiling studies. STRs are the first systems preferred in forensic science laboratories for identification purposes. However, genetic instability in tumoral tissues causes STR polymorphism to change, leading to erroneous results. On the other hand, insertion/deletion polymorphism (InDels) are used as genetic markers in forensic science, as they have features that make both STR and SNPs preferable. Although previous studies approved that STR instability is observed in many different tumors, there are only a few studies that have displayed the instability of InDels in tumoral tissues before. In this study, it was aimed to determine whether instability is observed in formalin-fixed paraffin-embedded breast and thyroid tumoral tissues at 36plex InDel Panel. A total of 47 cases, 26 of which were diagnosed as breast cancer and 21 as thyroid cancer, were included in the study. In 21 of 26 (80.76%) breast cancers mutational changes were observed, however only 6 of 21 (28.57%) thyroid carcinoma cases displayed instability.Moreover, in these six cases, mutations were detected at only 1 or 2 loci. The most common change in both tissues was loss of heterozygosity. These findings suggest that paraffin embedded tissues of thyroid tumor can be used in cases of forensic genetic identification, however paraffin embedded breast cancer tissues should be examined with care. In conclusion, low InDel mutation rates compared to STR instability, make InDel analysis from paraffin blocks suitable for forensic genetic identification. However, researchers should keep in mind that there may be differences between the profiles of the tumoral tissues taken as reference and the actual case. In addition, by incorporating additional markers such as SNPs and microhaplotypes with low mutation rates into the study alongside Indels, researchers can significantly enhance the discrimination power in identification processes.
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Short tandem repeat (STR) typing has been regularly used in paternity disputes and forensic human identification linked caseworks. Occasionally, forensic scientists come across aberrant allele patterns during STR typing because of mutations, genetic variations, and other abnormalities. The tri-allelic pattern of STR is rare, particularly, the case where this pattern exists at 4 loci. Here, we report the type II tri-allelic patterns observed at vWA, SE33, D8S1179, and D13S317 loci in the product of conception (POC) sample during the course of our regular paternity case investigation. The DNA extracted from the blood samples and tissue of POC were subjected to STR typing for autosomal and sex STR loci using the commercial QIAGEN's Investigator® IDplex Plus Kit and QIAGEN's Investigator® 24plex QS Kit. Capillary electrophoresis was carried out in 3500 and 3500xL Genetic Analyzer Applied Biosystems and genotyped using GeneMapper ID-X Software v1.5 and v1.6. In this case of paternity inclusion, the POC sample displayed type II tri-allelic patterns at vWA (16, 19, 20), SE33 (19, 28.2, 29.2), D13S317 (16, 19, 20), and D8S1179 (10, 13, 17) loci. In addition, the POC displayed an abnormal genotype with a heterozygous peak imbalance (type II-B) of (1:2) pattern at D3S1358, D21S11, and D16S539 loci, of (2:1) pattern at D1S1656, D12S391, D10S1248, D2S1338, D2S441, D18S317, FGA, CSF1PO, and D5S818 loci, and type II-C allelic pattern (one single peak with triplicate height) at D19S433 and DS7820 loci. Understanding of such anomalous genotypes improves the knowledge about tri-allelic pattern of CODIS loci and helps in the appropriate interpretation of the results in STR typing.
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The Han populations represent the largest ethnic group in China. Previous studies have primarily focused on investigating their genetic origins, migration and integration, as well as paternal genetic relationships within specific regional Han populations. However, a comprehensive analysis of the global paternal genetic structure of Han populations is lacking. In this study, we performed Y-chromosome sequencing on 362 unrelated male samples from Chinese Han individuals collected from Qinghai, Sichuan and Liaoning provinces. We then integrated relevant data from reported studies. Our final dataset comprised 1830 samples from 16 Han populations across 15 provinces in China, encompassing information on 89 Y-SNPs and 16 Y-STRs. Statistical analyses were conducted to assess Y-STR haplotype diversity (HD) and Y-SNP haplogroup frequencies. Additionally, we employed principal component analysis (PCA), phylogenetic tree and haplotype network to explore genetic differentiation within Han populations and the genetic relationships between Han populations and ethnic minorities surrounding them. Our results demonstrated that the O-M175 haplogroup represents the predominant paternal lineage in Han populations, with frequencies ranging from 60.53% (Qinghai Han) to 92.7% (Guangdong Han). Moreover, the subclades downstream of O-M175 showed distinct regional variations in their distribution patterns. The O2-M122 haplogroup was prevalent in all Han populations and demonstrated a gradual decline in frequency from north to south. Conversely, the distribution frequency of the O1b-M268 haplogroup decreased from south to north, particularly showed significant presence among Han populations in the Lingnan region. Haplogroup O1a-M119 distributed more frequently in the central Han populations. Our findings revealed that Chinese Han populations can be categorized into three subgroups: northern, central, and southern. Notably, there were significant differences among Han in Qinghai and other regions. Regarding the genetic relationships between Han populations and surrounding ethnic minorities, we observed a closer genetic affinity between different Han populations, but northern Han demonstrated a stronger relationship with the Hui ethnic group, while southern Han exhibited a closer connection with the Gelao and Li ethnic groups. In summary, this study presented a systematic analysis of haplogroup distribution, genetic substructure of Han populations and genetic relationships between Han populations and surrounding ethnic minorities based on 89 Y-SNPs and 16 Y-STRs systematically. Our research supplemented valuable insights into population genetics and forensic genetics, and provided data support for the forensic application of Y chromosome. The integration of Y-SNP haplogroups with Y-STR haplotypes offers enhanced understanding of the genetic substructure within Han populations, which holds significance for both population genetics research and forensic science applications.