Number Of Repeats Research Articles

Safety of gender affirming treatment in assigned female at birth transgender people and association of androgen and estrogen β receptor polymorphisms with clinical outcomes.

Gender affirming hormone treatment (GAHT) with androgens in assigned female at birth (AFAB) people with Gender Incongruence (GI) can induce and maintain variable phenotypical changes, but individual response may be genetically determined. To clarify the role of AR and ERβ polymorphisms we prospectively evaluated AFAB subjects undergoing virilizing GAHT. Fifty-two AFAB people with confirmed GI were evaluated before (T0) and after 6 (T6) and 12 months (T12) of testosterone enanthate 250 mg i.m. every 28 days. Hormone profile (testosterone, estradiol), biochemical (blood count, glyco-metabolic profile) and clinical parameters (Ferriman-Gallwey score, pelvic organs) were evaluated at each time-point, as well as number of CAG and CA repeats for AR and ERβ, respectively. All subjects have successfully achieved testosterone levels within normal male ranges and improved their degree of virilization, in absence of significant side effects. Hemoglobin, hematocrit and red blood cells were significantly increased after treatment, but within normal ranges. Ultrasound monitoring of pelvic organs showed their significant reduction already after 6 months of GATH, in absence of remarkable abnormalities. Furthermore, a lower number of CAG repeats was associated with a higher Ferriman-Gallwey score post treatment and a higher number of CA repeats was associated with uterine volume reduction. We confirmed safety and efficacy of testosterone treatment on all measured parameters. This preliminary data hints a future role of genetic polymorphisms to tailor GAHT in GI people, but evaluation on a larger cohort is necessary as the reduced sample size could limit data generalization at this stage.

Heterogenous Genetic, Clinical, and Imaging Features in Patients with Neuronal Intranuclear Inclusion Disease Carrying NOTCH2NLC Repeat Expansion.

Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disorder that is caused by the abnormal expansion of non-coding trinucleotide GGC repeats in NOTCH2NLC. NIID is clinically characterized by a broad spectrum of clinical presentations. To date, the relationship between expanded repeat lengths and clinical phenotype in patients with NIID remains unclear. Thus, we aimed to clarify the genetic and clinical spectrum and their association in patients with NIID. For this purpose, we genetically analyzed Japanese patients with adult-onset NIID with characteristic clinical and neuroimaging findings. Trinucleotide repeat expansions of NOTCH2NLC were examined by repeat-primed and amplicon-length PCR. In addition, long-read sequencing was performed to determine repeat size and sequence. The expanded GGC repeats ranging from 94 to 361 in NOTCH2NLC were found in all 15 patients. Two patients carried biallelic repeat expansions. There were marked heterogenous clinical and imaging features in NIID patients. Patients presenting with cerebellar ataxia or urinary dysfunction had a significantly larger GGC repeat size than those without. This significant association disappeared when these parameters were compared with the total trinucleotide repeat number. ARWMC score was significantly higher in patients who had a non-glycine-type trinucleotide interruption within expanded poly-glycine motifs than in those with a pure poly-glycine expansion. These results suggested that the repeat length and sequence in NOTCH2NLC may partly modify some clinical and imaging features of NIID.

Hypoxia controls expression of kidney-pathogenic MUC1 variants.

The interplay between genetic and environmental factors influences the course of chronic kidney disease (CKD). In this context, genetic alterations in the kidney disease gene MUC1 (Mucin1) predispose to the development of CKD. These variations comprise the polymorphism rs4072037, which alters splicing of MUC1 mRNA, the length of a region with variable number of tandem repeats (VNTR), and rare autosomal-dominant inherited dominant-negative mutations in or 5' to the VNTR that causes autosomal dominant tubulointerstitial kidney disease (ADTKD-MUC1). As hypoxia plays a pivotal role in states of acute and chronic kidney injury, we explored the effects of hypoxia-inducible transcription factors (HIF) on the expression of MUC1 and its pathogenic variants in isolated primary human renal tubular cells. We defined a HIF-binding DNA regulatory element in the promoter-proximal region of MUC1 from which hypoxia or treatment with HIF stabilizers, which were recently approved for an anti-anemic therapy in CKD patients, increased levels of wild-type MUC1 and the disease-associated variants. Thus, application of these compounds might exert unfavorable effects in patients carrying MUC1 risk variants.

RegCloser: a robust regression approach to closing genome gaps

BackgroundClosing gaps in draft genomes leads to more complete and continuous genome assemblies. The ubiquitous genomic repeats are challenges to the existing gap-closing methods, based on either the k-mer representation by the de Bruijn graph or the overlap-layout-consensus paradigm. Besides, chimeric reads will cause erroneous k-mers in the former and false overlaps of reads in the latter.ResultsWe propose a novel local assembly approach to gap closing, called RegCloser. It represents read coordinates and their overlaps respectively by parameters and observations in a linear regression model. The optimal overlap is searched only in the restricted range consistent with insert sizes. Under this linear regression framework, the local DNA assembly becomes a robust parameter estimation problem. We solved the problem by a customized robust regression procedure that resists the influence of false overlaps by optimizing a convex global Huber loss function. The global optimum is obtained by iteratively solving the sparse system of linear equations. On both simulated and real datasets, RegCloser outperformed other popular methods in accurately resolving the copy number of tandem repeats, and achieved superior completeness and contiguity. Applying RegCloser to a plateau zokor draft genome that had been improved by long reads further increased contig N50 to 3-fold long. We also tested the robust regression approach on layout generation of long reads.ConclusionsRegCloser is a competitive gap-closing tool. The software is available at https://github.com/csh3/RegCloser. The robust regression approach has a prospect to be incorporated into the layout module of long read assemblers.

Erectile function and androgen and estrogen beta receptor gene polymorphisms in acromegalic men

PurposeSexual dysfunctions are often experienced by male patients with acromegaly, due to a combination of hypogonadism and other comorbidities, but are a scarcely investigated complication. Erectile dysfunction is also closely related to cardiovascular diseases through endothelial dysfunction. Therefore, this project aimed to assess the prevalence of erectile dysfunction in a population of acromegalic men and evaluate its association with cardio-metabolic disorders, also exploring associations with androgen and estrogen receptor gene polymorphisms.MethodsSexually active men aged 18–65 with previous diagnosis of acromegaly were recruited. Clinical and laboratory data were retrospectively collected. Each patient also provided a blood sample for AR and ERβ gene polymorphisms analyses and filled out the IIEF-15 questionnaire.ResultsTwenty men with previous diagnosis of acromegaly (mean age 48.4 ± 10.0 years) were recruited. 13/20 subjects (65%) had erectile dysfunction, but only four had a concurrent biochemical hypogonadism, with no significant correlation with IIEF-15 scores. Total testosterone negatively correlated with sexual intercourse satisfaction domain (ρ = − 0.595; p = 0.019) and general satisfaction domain (ρ = − 0.651; p = 0.009). IGF-1 levels negatively correlated with biochemical hypogonadism (ρ = − 0.585; p = 0.028). The number of CAG and CA repeats in AR and ERβ receptors genes was not significantly associated with IIEF-15 scores or with GH/IGF-1 levels, but a negative correlation between CA repeats and the presence of cardiomyopathy (ρ = − 0.846; p = 0.002) was present.ConclusionsMen with acromegaly have a high prevalence of erectile dysfunction, but it does not appear to be correlated with treatments, testosterone levels and AR/ER-beta signaling. Nonetheless, a shorter CA polymorphic trait (ERbeta) is associated with the presence of cardiomyopathy. If confirmed, these data may suggest an association between an incorrect hormonal balance and increased cardiovascular risk in acromegaly subjects.

Identification of genetic relatedness of Mycobacterium ulcerans DNA from human and aquatic environmental samples: One Health approach to Buruli ulcer epidemiology

Buruli ulcer (BU) disease is a neglected tropical disease caused by Mycobacterium ulcerans (M. ulcerans) pathogen, an environmental mycobacterium, which has affinity to inhabit aquatic niches. This disease causes debilitation mostly in children between 3 to 15 years, preventing them from having smooth schooling. Currently, the integration of One Health approach in tackling health challenges is gaining momentum because of the obvious identification of linkages that would proffer more cost-effective and sustainable solution. In this study, the agent-host-environment molecular inter-relatedness in the transmission of Buruli ulcer disease in selected communities in Ogun State, Nigeria contiguous to Benin Republic; a BU epicentre was explored. Extraction of Mycobacterium ulcerans DNA from suspected BU patients, water samples from rivers routinely accessed by the patients and aquatic fauna (fish and crabs) from the same rivers was done. Variable Number of Tandem Repeats (VNTR) was amplified from the extracted DNA using primers targeting loci 6 and 19; genetic markers used in the study of M. ulcerans diversity. The findings revealed that locus 19 of the VNTR showed presence of M.ulcerans population in water, fish and human samples at the band size of 344bp. Locus 6 further confirmed the initial finding indicating the presence of M. ulcerans population at the band size of 510bp in fish, crab, water and human samples. There is an indication of plausible involvement of fish and crab (animal component), water (environmental component) and humans (host component) in the transmission of M. ulcerans pathogen. From the findings in this work, a possible transmission pathway of M. ulcerans to humans was proposed.

Tau deficiency protects human neurons from Abeta‐induced reduction of network activity

AbstractBackgroundOne hallmark of many neurodegenerative diseases, such as Alzheimer’s disease (AD), is the formation of neurofibrillary tangles by hyperphosphorylated Tau in the brain, resulting in neuronal death and cognitive decline. In the adult human brain, six Tau‐isoforms are expressed, originating from alternative splicing of exons 2, 3, and 10 of the MAPT gene. The isoforms differ in the number of N‐terminal inserts (0, 1, or 2N) and the C‐terminal repeat number (3 or 4R). Recent results from murine neurons highlight that the six human‐specific isoforms are differentially localized within neurons and influence microtubule dynamics in an isoform‐specific manner. In this study, we generated a human neuronal model system to further characterize the human‐specific Tau‐isoforms under basic and pathological conditions.MethodWe successfully generated three Tau KO hiPSC cell lines derived from Ngn2‐WTC11 cells using CRISPR/Cas9 and characterized the generated cell lines using genetic, biochemical and microscopy‐based methods.ResultNo difference between Tau KO and WT hiPSCs was observed in the capability of neuronal differentiation or neuronal morphology. Interestingly, Tau KO neurons were shown to be resistant to an Abeta‐induced reduction of network activity. Initial results from re‐expressed Tau‐isoforms in these neurons support the differential localization of the isoforms observed previously. Further experiments will investigate the isoform‐specific role of Tau regarding microtubule dynamics, axonal branching, and synapse formation under basal and pathological conditions.ConclusionTau KO hiPSCs are a versatile tool to study basic as well as pathological functions of Tau. Expected results will provide a major understanding of Tau function and help identifying potential therapeutic targets for the treatment of AD and related neurodegenerative diseases.

Association of Interleukin-1 Receptor Antagonist ( IL-1RA ) Gene Polymorphism with Community-Acquired Pneumonia in North Indian Children: A Case-Control Study.

Background Community-acquired pneumonia (CAP) is the leading cause of death in children < 5 years of age. The primary objective of the study was to assess the association of IL-1RA gene polymorphism in children aged 2 to 59 months with CAP and the secondary objective was to assess the association of gene polymorphism with mortality among hospitalized CAP cases. Study Design This case-control study was conducted in a tertiary teaching institute in Northern India. Hospitalized children aged 2 to 59 months with World Health Organization-defined CAP were included as cases after parental consent. Age-matched healthy controls were recruited from the immunization clinic of the hospital. Genotyping was done using polymerase chain reaction to analyze the variable number of tandem repeats of IL-1RA gene polymorphism. Result From October 2019 to October 2021, 330 cases (123, 37.27% female), and 330 controls (151, 45.75% female) were recruited. Genotype A2/A2 of the IL-1RA gene was found to be associated with the increased risk for CAP children with adjusted odds ratio (AOR) of 12.24 (95% confidence interval [CI] 5.21-28.7, p < 0.001). A2 and A4 alleles were also found to be at risk for CAP. A1/A2 genotype was found to be protective for CAP with an AOR of 0.29 (95% CI 0.19-19.0.45). The genotype A2/A2 and A2 allele of IL-1RA gene was associated with child mortality with CAP cases. Conclusion In IL1RA gene, A2/A2 genotype and A2 allele were associated with increased risk of CAP and A1/A2 were found to be protective for CAP. The genotype A2/A2 and A2 was associated with CAP mortality.

Dietary Patterns and Practices and Leucocyte Telomere Length: Findings from the UK Biobank.

Shorter telomere length (TL) is associated with risk of several age-related diseases and decreased life span, but the extent to which dietary patterns and practices associate with TL is uncertain. This study aimed to investigate the association of dietary patterns and practices and leucocyte TL (LTL). This was a cross-sectional study. Data collected voluntarily from up to 422,797 UK Biobank participants, during 2006-2010. LTL was measured as a ratio of the telomere repeat number to a single-copy gene and was loge-transformed and standardized (z-LTL). Adherence a priori to a Mediterranean-style diet was assessed through the MedDietScore. Principal component analysis was used to a posteriori extract the "Meat" and "Prudent" dietary patterns. Additional dietary practices considered were the self-reported adherence to "Vegetarian" diet, "Eating 5-a-day of fruit and vegetables" and "Abstaining from eggs/dairy/wheat/sugar." Associations between quintiles of dietary patterns or adherence to dietary practices with z-LTL were investigated through multivariable linear regression models (adjusted for demographic, lifestyle, and clinical characteristics). Adherence to the "Mediterranean" and the "Prudent" patterns, was positively associated with LTL, with an effect magnitude in z-LTL of 0.020 SD and 0.014 SD, respectively, for the highest vs the lowest quintile of adherence to the pattern (both P values < 0.05). Conversely, a reversed association between quintile of the "Meat" pattern and LTL was observed, with z-LTL being on average shorter by 0.025 SD (P= 6.12×10-05) for participants in the highest quintile of the pattern compared with the lowest quintile. For adherents to "5-a-day" z-LTL was on average longer by 0.027 SD (P= 5.36×10-09), and for "abstainers," LTL was shorter by 0.016 SD (P= 2.51×10-04). The association of LTL with a vegetarian diet was nonsignificant after adjustment for demographic, lifestyle, and clinical characteristics. Several dietary patterns and practices associated with beneficial health effects are significantly associated with longer LTL. However, the magnitude of the association was small, and any clinical relevance is uncertain.

The relationship between the number of CAG repeats and clinical manifestations: a survey of Chinese DRPLA family.

To describe the clinical, radiological, and genetic characteristics of a Chinese family with dentatorubropallidoluysian atrophy (DRPLA). Explore the distribution of CAG repeat size to the clinical features of patients. We collected the clinical symptoms and DNA analysis for the DRPLA gene was performed on the family members. DRPLA patients reported in the literature were reviewed to analyze the association between CAG repeat size and clinical features. Six family members were confirmed by genetic analysis. The number of CAG repeat in the proband, her sister, her grandmother, her father, her uncle, and her cousin, was determined respectively as 63, 75, 50, 50, 50, 54. In our family, the sister of the proband had the earliest onset age and the most severe clinical symptoms, followed by the proband, and other family members showed no obvious clinical symptoms. Consistent with the conclusion of previous studies, the more repeats CAG, the earlier the age of onset and the severer phenotypes are. We found six family members have CAG repeat expansion in the DRPLA gene on chromosome 12p13. Even in the same family, patients have different clinical presentations. The size of CAG repeats is negatively correlated with the age of onset and positively correlated with symptom severity. When the number of repeats is ≥ 63, the age at onset is < 21years old, and obvious clinical symptoms generally appear. It seems to say the more repeats CAG, the earlier the age of onset and the severer phenotypes are. With a small number of cases in our family, the conclusion that the more CAG repeats, the earlier the onset and the more severe the clinical symptoms cannot be fully proved.

Tau mutation S356T in the three repeat isoform leads to microtubule dysfunction and promotes prion-like seeded aggregation.

Tauopathies are a group of neurodegenerative diseases, which include frontotemporal dementia (FTD) and Alzheimer's disease (AD), broadly defined by the development of tau brain aggregates. Both missense and splicing tau mutations can directly cause early onset FTD. Tau protein is a microtubule-associated protein that stabilizes and regulates microtubules, but this function can be disrupted in disease states. One contributing factor is the balance of different tau isoforms, which can be categorized into either three repeat (3R) or four repeat (4R) isoforms based on the number of microtubule-binding repeats that are expressed. Imbalance of 3R and 4R isoforms in either direction can cause FTD and neurodegeneration. There is also increasing evidence that 3R tauopathies such as Pick's disease form tau aggregates predominantly comprised of 3R isoforms and these can present differently from 4R and mixed 3R/4R tauopathies. In this study, multiple mutations in 3R tau were assessed for MT binding properties and prion-like aggregation propensity. Different missense tau mutations showed varying effects on MT binding depending on molecular location and properties. Of the mutations that were surveyed, S356T tau is uniquely capable of prion-like seeded aggregation and forms extensive Thioflavin positive aggregates. This unique prion-like tau strain will be useful to model 3R tau aggregation and will contribute to the understanding of diverse presentations of different tauopathies.

Narrative Review: Update on the Molecular Diagnosis of Fragile X Syndrome.

The diagnosis and management of fragile X syndrome (FXS) have significantly improved in the last three decades, although the current diagnostic techniques are not yet able to precisely identify the number of repeats, methylation status, level of mosaicism, and/or the presence of AGG interruptions. A high number of repeats (>200) in the fragile X messenger ribonucleoprotein 1 gene (FMR1) results in hypermethylation of promoter and gene silencing. The actual molecular diagnosis is performed using a Southern blot, TP-PCR (Triplet-Repeat PCR), MS-PCR (Methylation-Specific PCR), and MS-MLPA (Methylation-Specific MLPA) with some limitations, with multiple assays being necessary to completely characterise a patient with FXS. The actual gold standard diagnosis uses Southern blot; however, it cannot accurately characterise all cases. Optical genome mapping is a new technology that has also been developed to approach the diagnosis of fragile X syndrome. Long-range sequencing represented by PacBio and Oxford Nanopore has the potential to replace the actual diagnosis and offers a complete characterization of molecular profiles in a single test. The new technologies have improved the diagnosis of fragile X syndrome and revealed unknown aberrations, but they are a long way from being used routinely in clinical practice.

The relationship between the aggrecan VNTR polymorphism and its content in lumbar intervertebral discs.

There is a specific polymorphism of the ACAN gene called the variable number of tandem repeats (VNTR), which is particularly interesting in the light of the development of intervertebral disc pathology and associated low back pain. The nucleus pulposus specimens were harvested from the L5/S1 intervertebral discs. The aggrecan content was determined using enzyme- linked immunosorbent assay (ELISA). Moreover, the VNTR polymorphism in the ACAN gene was evaluated. The genotyping of VNTR polymorphism in ACAN gene was successful in 94 tissue samples (48 homozygotes and 46 heterozygotes). The alleles were divided into four groups, in accordance with the number of tandem repeats in the ACAN gene. No difference between groups in the mean aggrecan mass nor in the mean degree of tissue moisture was observed. No relationship between the ACAN gene VNTR polymorphism and the aggrecan content was observed in studied Caucasian cadavers. Such a relationship may be a more complex phenomenon and exists in other populations.

Association of two variable number of tandem repeats in the monoamine oxidase A gene promoter with suicide completion: The present study and meta-analysis.

One potential cause of suicide is serotonergic dysfunction. Sex differences have been reported to modulate the effects of serotonergic polymorphisms. Monoamine oxidase A (MAOA) is an enzyme that degrades serotonin and is located on the X chromosome. A previous study indicated that the upstream (u) variable number of tandem repeat (VNTR) in the MAOA gene promoter may be associated with suicide. However, a meta-analysis showed that this polymorphism may not be related to suicide. According to a recent study, compared with the uVNTR, the distal (d)VNTR and the haplotypes of the two VNTRs modulate MAOA expression. We examined the two VNTRs in the MAOA gene promoter in 1007 subjects who committed suicide and 844 healthy controls. We analyzed the two VNTRs using fluorescence-based polymerase chain reaction assays. We conducted a meta-analysis for the two VNTRs to update it. Our results demonstrated that neither the genotype-based associations nor allele/haplotype frequencies of the two VNTRs were significantly associated with suicide. In the meta-analysis, we did not indicate relationships between uVNTR and suicide nor did we identify articles analyzing dVNTR in suicide. Overall, we did not find a relationship between the two VNTRs in the MAOA promoter and suicide completion; thus, warranting further studies are required.

Short Tandem Repeat DNA Profiling Using Perylene-Oligonucleotide Fluorescence Assay.

We report an amplification-free genotyping method to determine the number of human short tandem repeats (STRs). DNA-based STR profiling is a robust method for genetic identification purposes such as forensics and biobanking and for identifying specific molecular subtypes of cancer. STR detection requires polymerase amplification, which introduces errors that obscure the correct genotype. We developed a new method that requires no polymerase. First, we synthesized perylene-nucleoside reagents and incorporated them into oligonucleotide probes that recognize five common human STRs. Using these probes and a bead-based hybridization approach, accurate STR detection was achieved in only 1.5 h, including DNA preparation steps, with up to a 1000-fold target DNA enrichment. This method was comparable to PCR-based assays. Using standard fluorometry, the limit of detection was 2.00 ± 0.07 pM for a given target. We used this assay to accurately identify STRs from 50 human subjects, achieving >98% consensus with sequencing data for STR genotyping.

The prevalence and changes over time of equine glandular gastric disease in a teaching herd population

SummaryBackgroundThe natural progression of equine glandular gastric disease (EGGD) in the absence of treatment has not yet been described in the literature, nor has the prevalence in a teaching herd population been reported.ObjectivesThe aims of this study were to determine the prevalence of disease in a teaching population over the study period (2019–2021) and to observe the changes over time in disease severity of naturally occurring diseases (not experimentally induced) without medical intervention.MethodsTwenty‐one horses underwent an initial gastroscopy and a repeat gastroscopy between 14 and 731 days later. Gastroscopy data were graded quantitatively and described qualitatively. Prevalence and 95% confidence intervals (CI) were calculated. The changes over time were determined by comparing initial and repeat gastroscopies.ResultsThe prevalence from initial, repeat and total number of gastroscopies was 62% (95% CI: 40.8–79.3), 71% (95% CI: 50.0–86.2) and 67% (95% CI: 51.6–79), respectively. The changes over time included worsening of disease in 29% of horses (95% CI: 13.8–50.0), improvement of disease to a lower grade in 24% (95% CI: 10.6–45.1), no change in grade in 38% (95% CI: 20.8–59.1), and complete resolution of disease to grade 0 in 10% (95% CI: 2.7–28.9).Main limitationsLimitations included a maximum of two gastroscopies per horse given COVID‐19 restrictions on data collection, and highly varied interval times between initial and repeat gastroscopies.ConclusionIn conclusion, there is a high prevalence of disease in this teaching herd. The changes over time in naturally occurring diseases without medical intervention might include worsening, improvement, no change or resolution of disease.

QR code technology in individual identification training provides an introduction in hands-on forensic DNA genotyping to medical students

BackgroundForensic biology is a subject in the field of forensic science that stresses practical teaching and training in laboratory skills. Visualization of deoxyribonucleic acid (DNA) profiles is important in individual identification and is easily performed by well-trained examiners. Therefore, developing a novel training project for obtaining individual DNA profiles can improve the quality of teaching for medical students or trainees. DNA profiles based on quick response (QR) codes can also be applied to practical teaching and operation training for individual identification.MethodsA novel training project was developed through an experimental course in forensic biology. Blood samples and buccal swabs with oral epithelial cells, as used in the forensic DNA laboratory, were obtained from medical students at Fujian Medical University. DNA was isolated, and a number of short tandem repeat (STR) loci were used as genetic markers to generate DNA profiles. The students converted DNA profiles and individual information into a QR code. The QR code could then be scanned by a mobile phone for consulting and retrieval. Gene identity cards with QR codes were produced and provided to every student. The participation rate and passing rate of students who participated in the novel training project were calculated and compared with those of students in the traditional experimental course, and a chi-square test was carried out by SPSS 23.0 software to evaluate the teaching effectiveness. p < 0.05 indicated significant differences. In addition, a survey was conducted to investigate the likelihood of using of gene identity cards with QR codes in the future.ResultsA total of 54 of 91 medical students who studied forensic biology participated in the novel training project in 2021. Only 31 of 78 students who studied forensic biology participated in the traditional experimental course in 2020. The participation rate in the novel training project was 24% higher than that of the traditional experimental course. The participants in the novel training project showed better performance in forensic biological handling techniques. The passing rate of the students in the forensic biology course with the novel training project was approximately 17% higher than that of the students in the former course. The participation rates and passing rates of the two groups were significantly different (χ = 6.452, p = 0.008 and χ = 11.043, p = 0.001). In the novel training project, all participants made 54 gene identity cards with QR codes. Furthermore, in the DNA profiles of four African students who participated, we found two rare alleles that were not discovered in Asians. The survey showed that the use of gene identity cards with QR codes was accepted by most participants, and the likelihood of future utilization was 78%.ConclusionWe established a novel training project to promote the learning activities of medical students in experimental forensic biology courses. The participants showed great interest in using gene identity cards with QR codes to store general individual identity information and DNA profiles. They also examined the genetic population differences between different races based on DNA profiles. Hence, the novel training project could be useful for training workshops, forensic experimental courses, and medical big data research.

Machine Learning Approach for the Prediction of Age-Specific Probability of SCA3 and DRPLA by Survival Curve Analysis.

As the number of repeats in the expansion increases, polyglutamine diseases tend to show at a younger age. From this relationship, attempts have been made to predict age at onset by parametric survival analysis. However, a method for a more accurate prediction has been desirable. In this study, we examined 2 methods for survival analysis using machine learning and 6 conventional methods for parametric survival analysis of spinocerebellar ataxia (SCA)3 and dentatorubral-pallidoluysian atrophy (DRPLA). We compared the performance of 2 machine learning methods of survival analysis (random survival forest [RSF] and DeepSurv) and 6 methods of parametric survival analysis (Weibull, exponential, Gaussian, logistic, loglogistic, and log Gaussian). Training and evaluation were performed using the leave-one-out cross-validation method, and evaluation criteria included root mean squared error (RMSE), mean absolute error (MAE), and the integrated Brier score. The latter was used as the primary end point, and the survival analysis model yielding the best result was used to predict the asymptomatic probability. Among the models examined, the RSF and DeepSurv machine learning methods had a higher prediction accuracy than the parametric methods of survival analysis. For both SCA3 and DRPLA, RSF had a higher accuracy than DeepSurv for the assessment of RMSE (SCA3: 7.37, DRPLA: 10.78), MAE (SCA3: 5.52, DRPLA: 8.17), and the integrated Brier score (SCA3: 0.05, DRPLA: 0.077). Using RSF, we determined the age-specific probability distribution of age at onset based on CAG repeat size and current age. In this study, we have demonstrated the superiority of machine learning methods for predicting age at onset of SCA3 and DRPLA using survival analysis. Such accurate prediction of onset will be useful for genetic counseling of carriers and for devising methods to verify the effects of interventions for unaffected individuals.

Novel strategy of multiple-locus variable number tandem repeats analysis for genetic fingerprinting of human.

The variable number of tandem repeat (VNTR) analyses are methods based on the detection of repeated sequences within the human genome. In order to perform DNA typing at the personal laboratory, it is necessary to improve the VNTR analysis. The VNTR markers were difficult to popularize because PCR amplification was difficult due to its GC-rich and long nucleotide sequence. The aim of this study was to select the multiple VNTR markers that could only be identified by PCR amplification and electrophoresis. We genotyped each of the 15 VNTR markers using genomic DNA from 260 unrelated individuals by PCR amplification. Differences in the fragment length of PCR products are visualized by agarose gel electrophoresis. To confirm their usefulness as a DNA fingerprint these 15 markers were simultaneously analyzed with the DNA of 213 individuals and verified the statistical significance. In addition, to investigate the usefulness of each of the 15 VNTR markers as paternity markers, Mendelian segregation by meiotic division within a family consisting of two or three generations was confirmed. Fifteen VNTR loci selected in this study could be easily amplified by PCR and analyzed by electrophoresis, and were newly named DTM1 ~ 15. The number of total alleles in each VNTR showed from 4 to 16, and 100 to 1600bp in length, and their heterozygosity ranged from 0.2341 to 0.7915. In simultaneous analysis of 15 markers from 213 DNAs, the probability of chance appearing the same genotype in different individuals was less than 4.09E-12, indicating its usefulness as a DNA fingerprint. These loci were transmitted through meiosis by Mendelian inheritance in families. Fifteen VNTR markers have been found to be useful as DNA fingerprints for personal identification and kinship analysis that can be used at the personal laboratory level.

An escalating continuum of learning and attention difficulties from premutation to full mutation in female carriers of FMR1 expansion.

Carriers of Fragile X premutation may have associated medical comorbidities, such as Fragile X-associated tremor and ataxia (FXTAS) and Fragile X-associated premature ovarian insufficiency (FXPOI). We examined the Fragile X premutation effect on cognition, and we assumed that there is a direct correlation between the continuous spectrum of specific learning and attention deficits to the number of CGG repeats on the FMR1 gene. A total of 108 women were referred to our center due to a related Fragile X syndrome (FXS) patient, 79 women carried a premutation of 56-199 repeats, and 19 women carried a full mutation of more than 200 CGG repeats on FMR1 gene. Genetic results of CGG repeats, demographic information, structured questionnaires for ADHD, learning disabilities of language and mathematics, and independence level were analyzed in women carrying the FMR1 premutation and compared to the group carrying the full mutation. Women with FXS and FXTAS were excluded. When analyzed as a continuum, there was a significant increase in the following complaints which were associated with a higher number of repeats: specific daily function skills such as driving a car, writing checks, disorientation in directions, and also specific learning difficulties such as spelling and math difficulties. Additionally, when tested as a categorical independent variable, we observe that women with the full mutation were more likely to have ADHD or other learning disability diagnoses in the past than during premutation (<200 CGG repetitions). Specific learning and attention difficulties and resulting daily function difficulties correlate with an increased number of CGG repeats and are more likely to be associated as a common feature of premutation and full mutation in a female premutation carrier. Despite evidence of learning and attention difficulties, it is encouraging that most female carriers of the premutation and full mutation function well in most areas. Nevertheless, they face significant difficulties in specific areas of functioning such as driving, and confusion in times and schedules. Those daily function skills are mostly impacted by dyscalculia, right and left disorientation, and attention difficulties. This may aid to design specific interventions to address specific learning deficits in order to improve daily function skills and quality of life.