SNPscan as a high-performance screening tool for mutation hotspots of hearing loss-associated genes

SNPscan Combined With CNVplex as a High-Performance Diagnostic Method for Thalassemia

OBJECTIVE

Thalassemia is a Mendelian-inherited blood disorder with severe consequences, including disability and mortality, making it a significant public health concern. Therefore, there is an urgent need for precise diagnostic technologies. We introduce two innovative diagnostic techniques for thalassemia, SNPscan and CNVplex, designed to enhance molecular diagnostics of thalassemia.

METHODS

The SNPscan and CNVplex assays utilize variations in PCR product length and fluorescence to identify multiple mutations. In the SNPscan method, we designed three probes per locus: two 5' and one 3', and incorporated allele identification link sequences into one of the 5' probes to distinguish the alleles. The detection system was designed for 67 previously reported loci in the Chinese population for a specific genetic condition. CNVplex identifies deletion types by analyzing the specific positions of probes within the globin gene. This innovative approach enables the detection of six distinct deletional mutations, enhancing the precision of thalassemia diagnostics. We evaluated and refined the methodologies in a training cohort of 100 individuals with confirmed HBA and HBB genotypes. The validation cohort, consisting of 1647 thalassemia patients and 100 healthy controls, underwent a double-blind study. Traditional diagnostic techniques served as the control methods.

RESULTS

In the training set of 100 samples, 10 mutations (Hb QS, Hb CS, Hb Westmead, CD17, CD26, CD41-42, IVS-II-654, --SEA, -α3.7 and -α4.2) were identified, consistent with those identified by traditional methods. The validation study showed that SNPscan/CNVplex offered superior molecular diagnostic capabilities for thalassemia, with 100% accuracy compared to 99.43% for traditional methods. Notably, the assay identified three previously undetected mutations in 10 cases, including two deletion mutations (Chinese Gγ(Aγδβ)0 del and SEA-HPFH), and one non-deletion mutation (Hb Q-Thailand).

CONCLUSIONS

The SNPscan/CNVplex assay is a cost-effective and user-friendly tool for diagnosing thalassemia, demonstrating high accuracy and reliability, and showing great potential as a primary diagnostic method in clinical practice.

Polygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude

The adaptation of Tibetans to high-altitude environments has been studied extensively. However, the direct assessment of evolutionary adaptation, i.e., the reproductive fitness of Tibetans and its genetic basis, remains elusive. Here, we conduct systematic phenotyping and genome-wide association analysis of 2,252 mother-newborn pairs of indigenous Tibetans, covering 12 reproductive traits and 76 maternal physiological traits. Compared with the lowland immigrants living at high altitudes, indigenous Tibetans show better reproductive outcomes, reflected by their lower abortion rate, higher birth weight, and better fetal development. The results of genome-wide association analyses indicate a polygenic adaptation of reproduction in Tibetans, attributed to the genomic backgrounds of both the mothers and the newborns. Furthermore, the EPAS1-edited mice display higher reproductive fitness under chronic hypoxia, mirroring the situation in Tibetans. Collectively, these results shed new light on the phenotypic pattern and the genetic mechanism of human reproductive fitness in extreme environments.

Two MMP2 gene polymorphisms significantly associated with polycystic ovary syndrome: A case-control analysis

PURPOSE

To study the association between MMP2 gene polymorphisms (rs7201 and rs243849) and polycystic ovary syndrome (PCOS) risk.

METHODS

1287 participants, including 592 PCOS and 623 controls, were collected. In analysis, six genotype models (dominant model: MM + MW vs. WW; recessive model: MM vs. MW + WW; over-dominant model: MM + WW vs. MW; co-dominant model: MM vs. MW; co-dominant model: MM vs. WW; allele analysis: M vs. W, where M: minor allele; W: major allele) were applied. Subgroup analyses were performed based on race and obesity.

RESULTS

In the whole sample, only rs7201 was identified to protect from the PCOS (unadjusted: Recessive MM vs MW + WW, OR = 0.551, 95%CI = 0.311-0.974, P = 0.040; co-dominant MM vs WW, OR = 0.541, 95%CI = 0.304-0.964, P = 0.037). Subgroup analysis also identified rs243849 to be significantly associated with PCOS risk in the Han race (unadjusted: co-dominant MM vs WW, OR = 0.383, 95%CI = 0.153-0.961, P = 0.041; Allele M vs W, OR = 0.729, 95%CI = 0.553-0.963, P = 0.026). Moreover, rs243849 could regulate prominently MMP2 gene expression. However, no statistical significances were identified in the obesity groups (body mass Index and waist-hip ratio).

CONCLUSIONS

We identified for the first time that both rs7201 and rs243849 of MMP2 could protect from PCOS. Further studies with larger samples are needed to confirm the conclusion.

Association between AKT2 gene polymorphism and polycystic ovary syndrome: a case-control study

OBJECTIVE

This study was conducted to understand the association between the AKT2 (AKT serine/threonine kinase 2) gene polymorphism (rs2304186) and PCOS.

METHODS

In total, 1287 participants were included. Six genotype models (Dominant model: TT + TG vs. GG; Recessive model: TT vs. TG + GG; Over-dominant model: TT + GG vs. TG; Co-dominant model: TT vs. TG; Co-dominant TT vs. GG; Allele analysis: T vs. G) were applied in the analysis. According to the races and obesity, subgroup analyses were also performed.

RESULTS

No significant association between rs2304186 and PCOS was identified in the whole sample or the Han groups, even after multi-adjustments. Only in the Zhuang groups was it suggested that rs2304186 might promote the risk of PCOS to some extent (Unadjusted: Over-dominant TT + GG vs. TG, OR = 1.522, 95%CI = 1.076-2.152, p = .018; Age-adjusted: Over-dominant TT + GG vs. TG, OR = 1.543, 95%CI = 1.069-2.228, p = .021; Multi-adjusted: OR = 1.497, 95%CI = 1.024-2.188, p = .037). The risk effect was also detected in the non-obesity group (BMI <24.0 kg/m²) for the Co-dominant model (TT vs. TG: OR = 1.355, 95%CI = 1.001-1.835, p = .050).

CONCLUSIONS

In summary, we first discovered that rs2304186 might significantly elevate the PCOS risk, especially in the Chinese Zhuang population and the non-obesity group. Further studies are needed to confirm these results.

Polygenic Risk Score for Early Prediction of Sepsis Risk in the Polytrauma Screening Cohort

BACKGROUND

Increasing genetic variants associated with sepsis have been identified by candidate-gene and genome-wide association studies, but single variants conferred minimal alterations in risk prediction. Our aim is to evaluate whether a weighted genetic risk score (wGRS) that aggregates information from multiple variants could improve risk discrimination of traumatic sepsis.

METHODS

Sixty-four genetic variants potential relating to sepsis were genotyped in Chinese trauma cohort. Genetic variants with mean decrease accuracy (MDA) > 1.0 by random forest algorithms were selected to construct the multilocus wGRS. The area under the curve (AUC) and net reclassification improvement (NRI) were adopted to evaluate the discriminatory and reclassification ability of weighted genetic risk score (wGRS).

RESULTS

Seventeen variants were extracted to construct the wGRS in 883 trauma patients. The wGRS was significantly associated with sepsis after trauma (OR = 2.19, 95% CI = 1.53-3.15, P = 2.01 × 10-5) after being adjusted by age, sex, and ISS. Patients with higher wGRS have an increasing incidence of traumatic sepsis (P trend = 6.81 × 10-8), higher SOFA (P trend = 5.00 × 10-3), and APACHE II score (P trend = 1.00 × 10-3). The AUC of the risk prediction model incorporating wGRS into the clinical variables was 0.768 (95% CI = 0.739-0.796), with an increase of 3.40% (P = 8.00 × 10-4) vs. clinical factor-only model. Furthermore, the NRI increased 25.18% (95% CI = 17.84-32.51%) (P = 6.00 × 10-5).

CONCLUSION

Our finding indicated that genetic variants could enhance the predictive power of the risk model for sepsis and highlighted the application among trauma patients, suggesting that the sepsis risk assessment model will be a promising screening and prediction tool for the high-risk population.

Connexin Genes Variants Associated with Non-Syndromic Hearing Impairment: A Systematic Review of the Global Burden

Mutations in connexins are the most common causes of hearing impairment (HI) in many populations. Our aim was to review the global burden of pathogenic and likely pathogenic (PLP) variants in connexin genes associated with HI. We conducted a systematic review of the literature based on targeted inclusion/exclusion criteria of publications from 1997 to 2020. The databases used were PubMed, Scopus, Africa-Wide Information, and Web of Science. The protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number “CRD42020169697”. The data extracted were analyzed using Microsoft Excel and SPSS version 25 (IBM, Armonk, New York, United States). A total of 571 independent studies were retrieved and considered for data extraction with the majority of studies (47.8% (n = 289)) done in Asia. Targeted sequencing was found to be the most common technique used in investigating connexin gene mutations. We identified seven connexin genes that were associated with HI, and GJB2 (520/571 publications) was the most studied among the seven. Excluding PLP in GJB2, GJB6, and GJA1 the other connexin gene variants (thus GJB3, GJB4, GJC3, and GJC1 variants) had conflicting association with HI. Biallelic GJB2 PLP variants were the most common and widespread variants associated with non-syndromic hearing impairment (NSHI) in different global populations but absent in most African populations. The most common GJB2 alleles found to be predominant in specific populations include; p.Gly12ValfsTer2 in Europeans, North Africans, Brazilians, and Americans; p.V37I and p.L79Cfs in Asians; p.W24X in Indians; p.L56Rfs in Americans; and the founder mutation p.R143W in Africans from Ghana, or with putative Ghanaian ancestry. The present review suggests that only GJB2 and GJB3 are recognized and validated HI genes. The findings call for an extensive investigation of the other connexin genes in many populations to elucidate their contributions to HI, in order to improve gene-disease pair curations, globally.

Exome-Wide Association Analysis Suggests LRP2BP as a Susceptibility Gene for Endothelial Injury in Systemic Sclerosis in the Han Chinese Population

Genetic factors play a key role in the pathogenesis of autoimmune diseases, whereas the disease-causing variants remain largely unknown. Herein, we performed an exome-wide association study of systemic sclerosis in a Han Chinese population. In the discovery stage, 527 patients with systemic sclerosis and 5,024 controls were recruited and genotyped. In the validation study, an independent sample set of 479 patients and 1,096 controls were examined. In total, we found that four independent signals reached genome-wide significance. Among them, rs7574865 (P_combined = 3.87 × 10^-12) located within signal transducer and activator of transcription 4 gene was identified previously using samples of European ancestry. Additionally, another signal including three SNPs in linkage disequilibrium might be unreported susceptibility loci located in the epidermis differentiation complex region. Furthermore, two SNPs located within exon 3 of IGHM (rs45471499, P_combined = 1.15 × 10^-9) and upstream of LRP2BP (rs4317244, P_combined = 4.17 × 10^-8) were found. Moreover, rs4317244 was identified as an expression quantitative trait locus for LRP2BP that regulates tight junctions, cell cycle, and apoptosis in endothelial cell lines. Collectively, our results revealed three signals associated with systemic sclerosis in Han Chinese and suggested the importance of LRP2BP in systemic sclerosis pathogenesis. Given the limited sample size and discrepancies between previous results and our study, further studies in multiethnic populations are required for verification.

Association of Polymorphisms in Candidate Genes with the Litter Size in Two Sheep Breeds

Hu sheep and Small-tailed Han sheep are the most widely raised and most famous maternal sheep breeds in China, which are known for precocious puberty, perennial oestrus and high fecundity (1-6 lambs each parity). Therefore, it is crucial to increase litter size of these two breeds for intensive sheep industry. The objective of this study was to identify potential genetic markers linked with sheep litter size located at ten genes. This study collected blood sample of 537 Hu sheep and 420 Small-tailed Han sheep with litter size of first parity. The average litter sizes in Hu sheep and Small-tailed Han sheep were 2.21 and 1.93. DNA-pooling sequencing method was used for detecting the potential single nucleotide polymorphisms (SNPs) in ten genes related to follicle development and female reproduction. SNPscan® was used for individually genotyping. As a result, a total of 78 putative SNPs in nine out of ten candidate genes (except NOG) were identified. In total, 50 SNPs were successfully genotyped in Hu sheep and Small-tailed Han sheep. After quality control, a total of 42 SNPs in Hu sheep and 44 SNPs in Small-tailed Han sheep were finally used for further analysis. Association analysis revealed that nine SNPs within six genes (KIT: g.70199073A>G, KITLG: g.124520653G>C, ADAMTS1: g.127753565T>C, ADAMTS1: g.127754640G>T, NCOA1: g.31928165C>T, NCOA1: g.32140565G>A, LIFR: g.35862868C>T, LIFR: g.35862947G>T and NGF: g.91795933T>C) were significantly associated with litter size in Hu sheep or Small-tailed Han sheep. A combined haplotypes analysis of the two loci (LIFR: g.35862868C>T and LIFR: g.35862947G>T) revealed that H2H3 (CTTT) combined haplotypes had the largest litter size than the rest combined haplotypes and more than those with either mutation alone in Small-tailed Han sheep. Taken together, our study suggests that nine significant SNPs in six genes can be served as useful genetic markers for MAS in sheep.

Identification of Pathogenic Genes of Nonsyndromic Hearing Loss in Uyghur Families Using Massively Parallel DNA Sequencing Technique

We aim to identify the mutations of deafness genes using massively parallel DNA sequencing in the 12 Uyghur families. SNPscan method was used to screen against the 124 sites in the common deafness genes in probands. Subjects with SNPscan negativity were subject to massively parallel DNA sequencing for the sequencing of 97 genes known to be responsible for hearing loss. Eight families (66.7%) showed biallelic mutations in probands, including MYO15A mutation (6892C>T in J02 family, 9514C>T/7894G>T in J07 family, and 9514C>T in J16 family), MYO7A mutation (1258A>T in J03 family), TMC1 mutation (773G>A in J09 family and 1247T>G/1312G>A in J11 family), and PCDH15 mutation (4658delT in J08 and J13 families). Six novel types of mutation were identified including 6892C>T, 9514C>T/7894G>T, and 9514C>T in MYO15A gene, 1258A>T in MYO7A, 773G>A in TMC1, and 4658delT in PCDH15. The ratio of nonsense mutation and frameshift mutation was comparatively high. All these indicated that the mutation types reported in this study were rare. In conclusion, rare deafness genes were identified in the Uyghur families using massively parallel DNA sequencing, part of which were suggested to be related to the pathogenesis of the disease.

HIPK2 polymorphisms rs2058265, rs6464214, and rs7456421 were associated with kidney stone disease in Chinese males not females

BACKGROUND AND AIM

Recent studies have shown that genetic factors are involved in the development of kidney stone disease (KSD). A case-control association analysis was performed to investigate the association between homeodomain-interacting protein kinase 2 (HIPK2; OMIM *606868) polymorphisms and KSD.

METHODS

A total of 890 KSD patients and 920 healthy subjects were analyzed. Polymorphisms were genotyped using SNPscanTM high-throughput SNP classification technology. The genotypic and allelic frequencies in KSD patients and healthy individuals were analyzed using a Chi-square test.

RESULTS

The genotype and allele distributions of the three polymorphisms (rs2058265, rs6464214, and rs7456421 in HIPK2) displayed strong associations with KSD in males (rs2058265: odds ratio [OR] 2.480,95%confidence interval [CI] 1.205-5.106, p = 0.014; rs6464214: OR 2.466, 95%CI 1.198-5.078, p = 0.014; rs7456421: OR 2.846, 95%CI 1.362-5.947, p = 0.005; perallele: r2058265T, OR 1.357, 95%CI 1.073-1.715, p = 0.011; rs6464214G, OR 1.340, 95%CI 1.060-1.693, p = 0.014; rs7456421C, OR 1.356, 95%CI 1.073-1.713, p = 0.011). Patients carrying the T allele of rs2058265, the G allele of rs6464214, or the C allele of rs7456421 showed higher systolic blood pressure, creatinine, and uric acid levels compared with wild-genotype individuals after adjusting for age, gender, and body mass index (p < 0.005).

CONCLUSION

The association of HIPK2 gene polymorphisms with KSD was only observed in males but not in females. HIPK2 gene polymorphisms were also involved in the changes of KSD-related metabolic traits.

Association of genetic variation in B-cell activating factor with chronic hepatitis B virus infection

The outcome of hepatitis B virus (HBV) infection is considered to be related to the host immunogenetic susceptibility. B cell activating factor (BAFF) is involved in both B cell and T cell mediated immunity and its circulating levels were shown to be significantly elevated in HBV-related liver diseases. This study examined BAFF rs9514828 and rs12583006 polymorphisms in 386 patients with various liver diseases related to chronic HBV infection, 69 HBV infection resolvers, and 191 healthy controls. Both rs9514828 and rs12583006 polymorphisms and serum BAFF levels were determined in 232 patients with chronic HBV infection, and 61 healthy controls. The results showed that patients with chronic hepatitis had higher frequencies of rs9514828 genotype TT (19.75% vs. 11.86%, OR=2.397, 95% CI=1.121-5.125, P=0.023), genotypes CT+TT (74.69% vs. 63.55%, OR=1.478, 95% CI=1.050-2.080, P=0.045), and allele T (47.22% vs. 37.72%, OR=1.478, 95% CI=1.050-2.080, P=0.025) compared with patients with cirrhosis. Patients with chronic HBV infection and HBV infection resolvers had higher frequency of rs9514828 and rs12583006 haplotype TA compared with healthy controls (21.6% vs. 15.0%, OR=1.672, 95% CI=1.138-2.456, P=0.009 and 27.3% vs. 15.0%, OR=2.258, 95%CI=1.272-4.007, P=0.005, respectively). The rs9514828 and rs12583006 genotypes had no significant association with serum BAFF levels. These results suggest that the rs9514828 allele T may predispose to the liver inflammation in chronic HBV infection, and the rs9514828 and rs12583006 polymorphisms may combinatorially confer susceptibility to chronic HBV infection and resolution of the infection, possibly not through direct effect on serum BAFF levels.