Human Genetics最新文献

G-banded chromosome analysis, also known as G-banded karyotyping, remains a fundamental and irreplaceable diagnostic modality in clinical genetic testing. G-banded karyotypes provide whole genome visualization through chromosome banding patterns at the single-cell resolution for the diagnosis of chromosomal disorders. However, this method is labor-intensive and requires specialized expertise to manually analyze and karyotype metaphase spreads. In recent years, artificial intelligence (AI) algorithms have been utilized to automate karyotyping and assist with chromosome analysis. Despite this progress, there is a scarcity of studies evaluating the utility of artificial intelligence-assisted (AI-assisted) karyotyping analysis in cytogenetics diagnostic laboratories. This study highlights promising applications of AI-assisted karyotyping analysis in a cytogenetics diagnostic laboratory through a combination of a literature review, our data, and experience from a retrospective cohort study. This study also discusses important considerations of the use of AI-assisted karyotyping analysis in a cytogenetic diagnostic laboratory and outlines a two-stage framework for its implementation into clinical workflows. This approach aims to utilize the accuracy and efficiency of AI-assisted karyotyping analysis, potentially benefiting personalized patient care and contributing to advancements in the health system.

Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders influenced by environmental factors and characterised by a dysregulated immune response. DNA methylation (DNAm) a key epigenetic mechanism plays a role in the etiology of complex diseases like IBD. Epigenetic clocks which estimate biological aging through DNAm patterns have also been linked to various health states, including IBD. Previously, we profiled DNA methylation in peripheral blood from adult IBD patients and controls using the Illumina 450K microarray (n = 184). We now expand this dataset with 8-year clinical follow-up data, including disease progression and treatment response. Additionally, we generate second and third-generation epigenetic clock measures in this cohort to investigate if IBD patients exhibit epigenetic age acceleration compared to healthy controls. We identified one CpG site (cg03583111) significantly differentially methylated in IBD patients with long-term clinical recurrence (after the first year of study) compared to non-recurrence (no treatment escalation after 8 years). We assessed DNAm aging signatures in IBD patients versus controls, finding evidence of significant epigenetic age acceleration, as measured by three epigenetic clocks (GrimAge, GrimAge2, and DunedinPACE), in IBD patients compared to controls. These associations were replicated in two independent IBD cohorts: adult (GSE87648, n = 377) and paediatric (GSE112611, n = 238). Moreover, we observed higher age acceleration (GrimAge, U = 669, p = 0.003) and a faster pace of aging (DunedinPACE, t = 3.233, p = 0.002) in patients with active UC compared to inactive disease, but not for CD. These findings suggest that blood-based DNAm signatures could serve as biomarkers for detecting, monitoring, and classifying IBD.

Previous studies on Y-chromosomal haplogroup diversity in Poland have been focused mainly on macro-haplogroups. Consequently, younger subclades have rarely been explored to elucidate the relatively recent history of the Polish population. Here we present the results of deep genotyping of 598 chromosome Y sequences from modern Poland and demonstrate that about 60% of Polish males can be assigned to subhaplogroups that are both relatively young and widely distributed among different Slavic populations, thus supporting the scenario in which Early Slavic mass migration and territorial expansion took place in the first millennium of the common era. While most of those young Slavic-associated subclades are part of haplogroup R1a, other haplogroups, including I2a, R1b and E1b, are also represented by specific subclades, which together may constitute an important clue when trying to identify the location of the Proto-Slavic homeland based on ancient DNA data. Additionally, we have identified two specifically Polish subclades (I-Y6343 and R-Z17913, from haplogroups I1a and R1b, respectively) that likely descend from Late Ancient or Early Medieval founders representing the local Pre-Slavic population of the Roman period.

Despite advances in the genetic diagnosis of hearing loss, there remains room for improvement. One way to improve the genetic diagnostic rate is the proper assessment of synonymous variants that are often bioinformatically filtered out. We used GSDME as a model to demonstrate the importance of assessing synonymous variants. Variants in the gene GSDME (also known as DFNA5) are associated with autosomal dominant nonsyndromic hearing loss. The hearing loss is typically progressive and downsloping. All reported causative variants of GSDME-related hearing loss involve the skipping of exon 8, which results in the expression of a constitutively active, but truncated protein that induces apoptosis of cochlear hair cells. A retrospective search of previously tested patients identified 3 novel pathogenic synonymous GSDME variants. The functional impact of these variants was confirmed in vitro via a minigene splicing assay. We also observed variant-dependent differences in the levels of aberrant splicing, leading us to hypothesize that partial loss of splicing will result in a less severe hearing loss phenotype as compared to complete loss of splicing. Audiometric analysis found an association between complete loss of splicing and greater initial and/or more quickly progressing hearing loss as compared to partial loss of splicing. Over the course of the study, we also found limited correlation between in silico prediction and in vitro observed effects of a variant on splicing, indicating the need to cautiously apply in silico prediction tools in the context of genetic diagnosis.

A large proportion of individuals with celiac disease (CeD) remain undiagnosed, often presenting at an older age of onset or with non-classical symptoms compared to diagnosed cases. Such heterogeneity might be related to genetic factors. The aim was to utilize a CeD-screened adult population to compare the genetic variants in known and newly diagnosed cases. In the fourth wave of the population-based Trøndelag Health Study (HUNT4) 826 CeD and 51,516 non-CeD individuals were included. Medical registries identified 361 previously diagnosed cases, while screening identified 465 new cases. A validated polygenic risk score (PRS) was used to assess the genetic risk of CeD among the two case groups versus non-CeD individuals. Additional genetic variants not included in the PRS were also analyzed. The PRS distinguished cases from non-cases with high accuracy (AUROC: 85% for known cases, 83% for new cases). The genetic variation explained by the PRS was similar for known and new cases (17.1% versus 14.5%). The odds ratio for being in the highest genetic risk group (top 10%) was 22.7 (95% CI 14.1-36.4) for known cases and 18.6 (95% CI 12.4-27.9) for new cases versus the median group (40%-60%). Differences in effect size among specific genome-wide variants were observed but were not significantly associated with CeD. A validated PRS showed significant genetic difference between CeD cases and the general population, with similar association in both known and newly diagnosed cases. This suggests that genetic architectures of the two groups are comparable, implying that other non-genetic factors may drive CeD in adults.

Degraded samples pose a challenge in routine forensic practice. The commonly used short tandem repeat markers are not optimally suitable for the analysis of degraded samples because of their structural complexity and locus length. By contrast, single nucleotide polymorphisms (SNPs), characterised by their single base mutation feature, enable the design of short amplification fragments, conferring an advantage in detecting mutations in degraded samples. Hence, our team has developed a multiplex amplification system for individual identification of degraded samples, encompassing 507 autosomal SNP loci, five Y-InDel loci, and one amelogenin sex determination locus. The amplification fragment lengths in this multiplex system range from 81 to 116 bp. The forensic applicability of this panel was validated through sequencing analysis of 201 samples. Among these were 30 degraded samples (simulated degraded samples: heat degradation and ultrasonic fragmentation; formalin-fixed, paraffin-embedded samples). The results indicated that the genotyping accuracy of all loci included in this panel remained at 100% for samples with 0.1 ng of DNA input and severe degradation. Sensitivity experiments revealed that at a DNA input of only 31.25 pg, the locus detection rate reached 100%, with genotype accuracy of 92.5%. Based on population data analysis, the total discrimination power of this system reached 1-5.513 × 10^-143. Furthermore, we included forensic case samples encompassing semen, saliva, menstrual blood, 10-year-old bloodstain cards, and 12-year-old bloodstain cards in the validation studies. The results demonstrated 100% genotyping accuracy across all sample types. Additional, validation data confirmed the system's species specificity (Homo sapiens-specific) and tolerance to inhibitors including humic acid, heme, ethylene diamine tetraacetic acid and indigo (up to 200 µM). In conclusion, this system can serve as a novel tool for the analysis of degraded samples in forensic work.

Microtia-anotia is a common congenital anomaly. In most cases, the genetic etiology remains unknown. The proper development of outer ear is closely related to cranial neural crest cells. Abnormal DNA recombination perturbing the function of long-range enhancers can lead to genomic disorder. Previously, we identified 4p16.1 duplications in microtia patients and revealed the enhancer function of an evolutionarily conserved region (ECR). Here we recruited additional patients and attempted to identify the minimal overlapping region and regulatory elements. We identified five individuals (F6-F10 probands) with 4p16.1 duplication. The duplications in F3 and F5 were refined to 192.6 kb and 96.1 kb. Precise junction breakpoints in F4 and F6-F10 were detected. The minimal overlapping region (chr4: 8,689,510-8712,827, hg19) contained conserved sequences in addition to ECR. Dual-luciferase assays detected enhancer activity in the TFAP2C binding and 1794 sequence. We present five additional cases of concha-type microtia with 4p16.1 duplication. The minimal overlapping region contains regulatory elements that function as in-cis tissue-specific modules, regulating downstream gene expression during development of cranial neural crest cell.