SNaPshot Minisequencing Research Articles

#382 Unexpected diagnoses of ADTKD-MUC1 with the help of VNtyper

Abstract Background and Aims Autosomal dominant tubulointerstitial kidney disease (ADTKD) due to pathogenic variants in the MUC1 gene is difficult to diagnose since these variants lie in a large variable number tandem repeats (VNTR) and require specialized genetic testing, such as SNaPshot minisequencing. We recently developed a computational pipeline, VNtyper, for easier reliable detection of MUC1 VNTR pathogenic variants and have applied this tool to a large cohort of patients with various phenotypes of kidney disease. The aim of this study is to clinically describe patients in whom MUC1 pathogenic variants were unexpectedly detected with the help of VNtyper. Method We applied a computational pipeline, VNtyper, to a large cohort of patients with suspected hereditary kidney disease referred for genetic testing, regardless of their phenotype. This cohort included patients evaluated from 2017 to 2023 in the Molecular Genetics Department of Necker-Enfants Malades Hospital (Paris, France). Clinical characteristics were collected from patients in whom we detected new MUC1 VNTR pathogenic variants. Results 44 out of 3735 patients tested (1.2%) were newly diagnosed with a MUC1 pathogenic variant. Of these patients, ADTKD was clinically suspected in only 31 out of 44 patients (70%). In 2 patients, there was a pathogenic variant in another gene that could explain the phenotype, in addition to the MUC1 pathogenic variant. In fact, one 52-year-old patient had polycystic kidneys, nephrolithiasis, hematuria and normal kidney function. Her mother also had kidney cysts with absence of chronic kidney disease (CKD). This patient had a pathogenic variant in IFT140 gene (c.2399+1G>T) which could explain her autosomal dominant polycystic kidney disease (ADPKD) phenotype. Whether the MUC1 variant contributes to her disease remains unclear, especially seeing as her kidney function is normal at the age of 52 years. On the other hand, one patient had kidney cysts discovered at 3 days of age. A heterozygous HNF1B deletion was detected which could explain the phenotype. The following detection of a pathogenic MUC1 variant was thus an incidental finding and seemed de novo, although parents declined to get tested. These incidental findings can be challenging, especially when it comes to counselling and follow-up. There was no family history of kidney disease in 7 out of 44 patients (16%), and in one patient, we were able to confirm de novo disease since her parents were tested and were negative. It was unfortunately not possible to get DNA from the parents of the other patients. This is the first case of proven de novo ADTKD-MUC1 described to our knowledge. De novo variants in ADTKD-MUC1 are not surprising since the 7C stretch found in VNTR is a hotspot for mutagenesis. Interestingly, these patients seemed to have a more severe clinical presentation with an early onset of disease (median age at diagnosis 28 years [18, 32]). However, this could be due to a selection bias. In fact, young age of onset of CKD may have prompted clinicians to refer these patients for genetic testing despite negative family history, whereas older patients with possible ADTKD-MUC1 and no family history of kidney disease might be presumed to have another etiology of CKD. One way to confirm this would be to test a large cohort of patients with CKD from unknown etiology with no family history of CKD. Considering the nonspecific clinical manifestations of ADTKD-MUC1 and the phenotypic variability, it has previously been suggested that the most important clue to diagnosis is the presence of CKD in first-degree family. The possibility of de novo cases makes the clinical diagnosis of ADKTD-MUC1 even more challenging. Conclusion With VNtyper, we were able to diagnose new cases of ADTKD-MUC1 in a large cohort of patients with various phenotypes, with a significant prevalence of 1.2%. ADTKD-MUC1 was not suspected in 30% of these patients who would have maybe never been diagnosed otherwise. This is also the first study in which we describe a proven de novo case of ADTKD-MUC1. Pathogenic variants in the MUC1 gene should thus be in the differential diagnosis of all unspecified CKD, even if there is no family history since de novo variants are also possible.

#276 ADTKD genetic diagnostics in Europe: where do we stand and what is needed?

Abstract Background and Aims We are the first European patient organization to pursue the goal of raising awareness of the monogenic kidney disease ADTKD (autosomal dominant tubulointerstitial kidney disease) and supporting its research (www.adtkd.de/en-gb). To date, causative mutations are known in at least five disease genes (UMOD, MUC1, REN, HNF1B, SEC61A1) [1] and one can expect that even more disease genes exist. There are already strong international collaborations to define the clinical course of ADTKD [2] and to evaluate a targeted therapy in clinical trials [3]. Clinical registries form the basis for the inclusion of patients, preferably at an early stage of the disease. Such a registry already exists in the USA and is currently being established in Europe (ADTKD-Net) as part of the European Joint Program on Rare Diseases (EJP RD). Due to its non-specific and variable clinical characteristics, ADTKD is often misdiagnosed or not diagnosed at all. Experts therefore suspect a high number of unreported cases. There are also challenges in genetic diagnostics. While next generation sequencing (NGS) panels have been established for ADTKD, they are usually unable to detect pathogenic MUC1 variants due to their specific location in the genome. This is the insertion of an additional cytosine (dupC) in a VNTR (Variable Number of Tandem Repeats) domain of the MUC1 gene, which cannot be detected by NGS and therefore requires special procedures such as SnaPshot Minisequencing [4] or VNtyper [5]. For instance, there are only two laboratories that can perform this specific MUC1 testing in Germany to date. The aim of this study is to assess the status quo of ADTKD diagnostics in Europe. We hypothesize that there is a lack of appropriate structures to adequately and reliably diagnose ADTKD, notably ADTKD-MUC1. The study is intended to help identify deficits and obstacles in order to address these in a targeted manner. Methods We used Survey Monkey to create a digital survey, which we sent by email to around 50 European ADTKD experts. They were asked to answer 7 key questions (Fig. 1). For the selection of suitable ADTKD experts, we use various sources such as publications on ADTKD in PubMed, the Expert Finder and the European Patient Advocacy Groups (ePAG) in the European Reference Network for Rare Kidney Diseases (ERKNet) and our own network. Our aim is to cover at least the 30 largest countries in Europe in terms of population. Results Results will be presented at the ERA conference. Conclusion With our survey we would like to substantiate the hypothesis that the possibilities of molecular diagnostics of ADTKD in Europe are currently insufficient. Based on our results, short and long-term measures should be taken to remedy potential deficits so that as many patients as possible can be identified and have access to therapeutic options in the future. Another interesting aspect is the awareness of ADTKD among European nephrologists. This could be a future activity of our patient organization.

Multiplex Snapshot minisequencing for detection of common PAH gene mutations in Iranian patients with Phenylketonuria.

Phenylketonuria (PKU) is one of the most common inborn faults of amino acid metabolism in the world. It is caused by an autosomal recessive insufficiency of the hepatic enzyme phenylalanine hydroxylase (PAH) that catalysis the irreversible hydroxylation of phenylalanine to tyrosine. More than 950 different disease-causing mutations in the PAH gene have been identified. The most prominent complication of PKU if not diagnosed and treated is severe mental retardation. Early diagnosis and initiation of nutritional therapy are the most important measures in preventing this mental retardation. For this reason, we developed a simple and rapid molecular test for detection of the most frequent phenylalanine hydroxylase mutations. We have developed a PCR multiplex SNaPshot reaction that targets all 10 common mutations identified in PAH gene. Multiplex assays based on the SNaPshot minisequencing approach were developed to simultaneous genotype ten mutations at the PAH gene. We have optimized the detection of this mutations in one multiplex polymerase chain reaction (PCR) followed by ten single-nucleotide extension reactions. The different genotypes were determined based on the position and the fluorescent color of the peaks in a single electropherogram. DNA sequencing assay also were used to verify genotyping results obtained by SNaPshot minisequencing, all mutations were concordant. This method can be useful as secondary test in neonatal screening for hyperphenylalaninemia in neonates with a positive screening test and also be suitable for carrier screening. The assay can be easily applied for accurate, time and cost efficient genotyping of the selected SNPs in various populations.

Association of selected genetic variants in CBS and MTHFR genes in a cohort of children with homocystinuria in Sri Lanka

BackgroundHomocystinuria is an inherited, inborn error of homocysteine metabolism, which leads to the abnormal accumulation of homocysteine and its metabolites in blood and urine, resulting in various complications. Variants in the cystathionine β-synthase (CBS) and methylenetetrahydrofolate reductase (MTHFR) genes interrupt the formation of the corresponding enzymes and prevent homocysteine from being metabolised; hence, the homocysteine levels in plasma increase than the optimum levels. Materials and methodsIn the current study, eight clinically confirmed children with homocystinuria were detected to study the chosen variants in the CBS gene (c.833 T>C and c.19del) and in the MTHFR gene (c.665 C>T, c.1286 A>C) using SNaPshot mini-sequencing and direct sequencing. ResultsAfter screening eight patients, none had the c.833T>C, but four patients were in the homozygous state for the c.19del variant in the CBS gene. Furthermore, seven were heterozygous for c.1286A>C, while one patient was heterozygous for c.665C>T in the MTHFR gene. ConclusionAccording to the results, c.19del is common in the studied cohort of Sri Lankan children, while c.833T>C is absent, whereas c.1286A>C was more frequent than c.665C>T. To our knowledge, the current study was the first report to discuss the genetic impact of homocystinuria in Sri Lanka; further comprehensive studies are necessary with a larger sample size to establish the association of these variants with the disease in Sri Lanka, which can be beneficial in enhanced patient care and for prospective studies.

Single Nucleotide Polymorphisms Of Transforming Growth Factor-Β1 Gene As Potential Asthma Susceptible Variants In Punjabi Population Of Pakistan.

Candidate gene approach based on case-control model is a valuable strategy to determined disease related genetic variants. Two single nucleotide polymorphisms rs1800469 and rs2241715 in TGF β1gene have been reported to affect the asthmatic status in different populations. The main focus of this research was to find any relationship between these SNPs and asthma in Pakistani population. Using case-control model, a total of 108 individuals including 52 asthma patients and 56 healthy controls were screened to find asthma susceptibility of variants rs1800469 and rs2241715. These SNPs were genotyped using SNaPshot minisequencing assay followed by capillary electrophoresis using ABI 3130xl genetic analyzer platform. The statistical analysis of genetic data was performed by using SPSS 21, SHEsis online platform and SNPStats online web software. No association with asthma was seen in allelic model for both SNPs but genotypes analyzed under codominant, dominant, over dominant and recessive models of inheritance revealed that SNP rs2241715 is strongly associated with asthma under genotypic model. rs2241715 was found to be a genetic risk factor for asthma in Pakistani population.

Diverse molecular causes of unsolved autosomal dominant tubulointerstitial kidney diseases

Autosomal Dominant Tubulointerstitial Kidney Disease (ADTKD) is caused by mutations in one of at least five genes and leads to kidney failure usually in mid adulthood. Throughout the literature, variable numbers of families have been reported, where no mutation can be found and therefore termed ADTKD-not otherwise specified. Here, we aim to clarify the genetic cause of their diseases in our ADTKD registry. Sequencing for all known ADTKD genes was performed, followed by SNaPshot minisequencing for the dupC (an additional cytosine within a stretch of seven cytosines) mutation of MUC1. A virtual panel containing 560 genes reported in the context of kidney disease (nephrome) and exome sequencing were then analyzed sequentially. Variants were validated and tested for segregation. In 29 of the 45 registry families, mutations in known ADTKD genes were found, mostly in MUC1. Sixteen families could then be termed ADTKD-not otherwise specified, of which nine showed diagnostic variants in the nephrome (four in COL4A5, two in INF2 and one each in COL4A4, PAX2, SALL1 and PKD2). In the other seven families, exome sequencing analysis yielded potential disease associated variants in novel candidate genes for ADTKD; evaluated by database analyses and genome-wide association studies. For the great majority of our ADTKD registry we were able to reach a molecular genetic diagnosis. However, a small number of families are indeed affected by diseases classically described as a glomerular entity. Thus, incomplete clinical phenotyping and atypical clinical presentation may have led to the classification of ADTKD. The identified novel candidate genes by exome sequencing will require further functional validation.

Association Study of Mitochondrial DNA Haplogroup D and C5178A Polymorphisms with Chronic Kidney Disease.

Objective: To explore the associations of common mitochondrial DNA polymorphisms with chronic kidney disease (CKD). Methods: Data from 286 longevous individuals aged 95 years or older from the longevity arm from the Rugao Longevity and Ageing Study (RuLAS) were used. Twenty-eight common haplogroups defined by 33 single nucleotide polymorphisms were genotyped using SNaPshot minisequencing reaction assays. The creatinine-based estimated glomerular filtration rate (eGFR) was calculated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation. Results: The prevalence of CKD was 23.6% among the longevous participants aged 95 years and older. The D haplogroup (67.37 ± 14.72 vs. 70.65 ± 11.07, p = 0.045), the D5 haplogroup (60.86 ± 18.36 vs. 70.34 ± 11.53, p = 0.002), and the 5178A allele (67.23 ± 14.48 vs. 70.75 ± 11.10, p = 0.029) were associated with lower eGFR levels compared with noncarriers. The D5 haplogroup (13.8% vs. 3.6%, p = 0.005) was significantly higher, while D haplogroup (35.4% vs. 24%, p = 0.067) and the 5178A allele (36.9% vs. 24.9%, p = 0.056) were borderline significantly higher in CKD individuals than those without CKD. Further, after adjusting for multiple covariates, the D haplogroup, the D5 haplogroup, and the 5178A allele were associated with increased odds of CKD with odds ratios of 1.93 (95% confidence interval [CI]: 1.00-3.72, p = 0.050), 4.76 (95% CI: 1.49-15.22, p = 0.009) and 2.04 (95% CI: 1.05-3.96, p = 0.035), respectively. Conclusions: The D and D5 haplogroups, as well as the 5178A allele are associated with decreased eGFR levels and an increased risk of CKD in a longevous population.

A Candidate Gene Association Study for Economically Important Traits in Czech Dairy Goat Breeds.

Simple SummaryThe milk production traits of goats are economically important. In the Czech Republic, goat milk is processed directly on farms and distributed as cheese. Although goat breeding is not a main focus of animal production in the Czech Republic, it is essential for the agricultural sector. A group of 14 SNPs (single-nucleotide polymorphisms) within four candidate genes (ACACA, BTN1A1, LPL, and SCD) were analysed in two Czech dairy goat breeds, White Shorthaired (WSH) goats and Brown Shorthaired (BSH) goats. The SNPs were significantly associated with milk-production traits (daily milk yield, protein, and fat percentage) and somatic cell count. This information may be useful for marker-assisted selection or related techniques to increase the accuracy of selection.Milk production is influenced by many factors, including genetic and environmental factors and their interactions. Animal health, especially udder health, is usually evaluated by the number of somatic cells. The present study described the effect of polymorphisms in the ACACA, BTN1A1, LPL, and SCD genes on the daily milk yield, fat, and protein percentages and somatic cell count. In this study, 590 White Shorthaired (WSH) and Brown Shorthaired (BSH) goats were included. SNP genotyping was performed by PCR-RFLP and multiplex PCR followed by SNaPshot minisequencing analysis. The linear mixed model with repeated measurement was used to identify the genetic associations between the studied genes/SNPs and chosen traits. All selected genes were polymorphic in the tested goat populations and showed significant associations with milk traits. Only BTN1A1 (SNP g.599 A > G) showed a significant association with the somatic cell score. After Bonferroni correction, a significant effect of LPL g.300G > A on daily milk yield and fat percentage, LPL g.185G > T on protein percentage, and LPL G50C, SCD EX3_15G > A, and SCD EX3_68A > G on fat percentage was found. The importance of environmental factors, such as the herd-year effect, month of milking, and lactation order on all milk performance indicators was confirmed.

Genetic Susceptibility to Systemic Sclerosis in the Greek-Cypriot Population: A Pilot Study.

Background: Systemic Sclerosis (SSc), also known as scleroderma, is an autoimmune rheumatic disease, which is clinically subdivided into two major subgroups; limited (lcSSc) and diffuse cutaneous scleroderma (dcSSc). Even though the SSc etiologies remains unclear, some HLA and non-HLA genetic variants have been associated with the disease.Aim: This study was designed to evaluate the associations between several HLA-related genetic variants and SSc in the Greek-Cypriot population.Methods: Forty-one SSc patients and 164 controls were genotyped at 18 selected single nucleotide polymorphisms (SNPs) using restriction fragment length polymorphism analyses, Sanger sequencing, and a multiplex SNaPshot minisequencing assay. Logistic regression analysis under the log-additive model was used to evaluate all possible associations between these SNPs and SSc; nominal statistical significance was assumed at p < 0.05.Results: Associations of SSc with SNPs rs3117230, rs3128930, and rs3128965 within the HLA-DPB1 and HLA-DPB2 regions were observed in the Greek-Cypriot population at the level of p < 0.05. However, none of these associations survived a Bonferroni correction. The direction of the effect is consistent with the direction reported in previous studies. In addition, allele frequencies of the majority of the selected SNPs in the Greek-Cypriot population are similar to those reported in the European population.Conclusion: This study initiates the genetic investigation of SSc in the Greek-Cypriot population, a relatively small newly investigated population. Further investigation with a larger sample size and/or additional SSc susceptibility loci may confirm the association of some of these variants with SSc in the Greek-Cypriot population that could potentially be used for predictive testing.

Association between variant alleles of major histocompatibility complex class II regulatory genes and nasopharyngeal carcinoma susceptibility.

Major histocompatibility complex (MHC) class II regulatory genes play a paramount role in immune response that can exert a predominant influence on clinical outcome of Epstein-Barr virus infection consistently assumed as the main pathogenetic factor for nasopharyngeal carcinoma. To elucidate the relationship between allelic variants of MHC class II regulatory genes and susceptibility to nasopharyngeal carcinoma, a total of 28 polymorphic loci at MHC class II regulatory genes, involving CIITA, CREB1, RFX family genes (RFX5, RFXAP, and RFXANK), and NFY family genes (NFYA, NFYB, and NFYC), were genotyped by multiplex SNaPshot minisequencing in 137 patients with nasopharyngeal carcinoma and 107 healthy controls from the southern Chinese population. Allelic analysis disclosed that rs7404873, rs6498121, rs6498126, and rs56074043 shared correlations with nasopharyngeal carcinoma (Ptrend < 0.05). Further, rs6498126 on CIITA was independently associated with the risk of developing nasopharyngeal carcinoma (CC vs. GG, odds ratio: 7.386, 95% confidence interval: 1.934-28.207, Ptrend < 0.01). Conversely, rs7404873 on CIITA and rs56074043 on NFYB manifested epistatic interaction to decreased susceptibility of nasopharyngeal carcinoma (rs7404873, TT vs. GG, odds ratio: 0.256, 95% confidence interval: 0.088-0.740, Ptrend < 0.05; rs56074043, AA vs. AG, odds ratio: 0.341, 95% confidence interval: 0.129-0.900, Ptrend < 0.05). Additionally, bioinformatics analysis revealed that the three variants were transcriptional regulatory in function and might impact the expression of nearby genes. The findings suggested genetic variants on MHC class II regulatory genes contributed to nasopharyngeal carcinoma susceptibility and might provide new insights for screening high-risk population.

Network Analysis of Y-STR in Six Ethnic Populations in Guangxi and Its Forensic Significances.

Objective To explore the distribution of genetic structure of Y-SNP and Y-STR genetic markers in different ethnic groups and its application in forensic science. Methods SNaPshot minisequencing was used to detect the polymorphisms of 12 Y-SNP loci in 439 males from 6 ethnic groups, including Guangxi Han, Guangxi Jing, Guangxi Miao, Guangxi Yao, Guangxi Zhuang and Guangxi Dong. DNATyperTM Y26 kit was used to multiplex-amplify 26 Y-STR loci. The PCR products were analyzed by 3130xl genetic analyzer. The network analysis of Y-STR haplotype under the same Y-SNP haplogroup was analyzed by Network 5.0 software. Results Six haplogroups defined by 12 Y-SNP loci were detected in 6 ethnic groups, and 362 haplotypes were detected in 26 Y-STR loci. The haplotype diversity was 0.996 6. In the C haplogroup, the samples from Guangxi Yao, Guangxi Zhuang and Guangxi Dong were clustered on different branches; in the O1 haplogroup, those from Guangxi Zhuang, Guangxi Miao and Guangxi Jing were relatively independent and clustered separately; in the O2 haplogroup, some samples from Guangxi Miao and Guangxi Yao were gathered in a cluster. Conclusion Based on the Y-STR network analysis of samples with identical haplogroup of Y-SNP, some ethnic groups can be preliminarily distinguished, which could be used to infer male suspects' ethnic group through detecting their genetic markers left in the crime scene.

Sex-linked markers in pistachio

DNA markers have potential to improve the efficiency of conventional plant breeding via marker-assisted selection (MAS). Therefore, MAS can be very effective in pistachio to eliminate undesirable progenies at early stage which can save time, cost, labor, and land. This study aimed to develop sex-linked single nucleotide polymorphism (SNP) markers for MAS, to understand sex determination system and to determine the position of sex locus in pistachio. Eight male and eight female F1 progenies from 'Siirt' × 'Bagyolu' cross, along with the parents, were subjected to RAD (restriction site-associated DNA) sequencing and 38 SNP loci were detected as putative sex-associated ones in pistachio. Validation was performed by SNaPshot minisequencing analysis in mature F1 progenies and in a wide germplasm collection. Seventeen loci successfully distinguished sex in pistachio. To ascertain cost-effective application of markers in a breeding program, high-resolution melting (HRM) analysis was performed; and 10 markers were found to perfectly separate sexes in pistachio. Because of the female heterogamety in all sex-linked SNP loci, pistachio has a ZZ/ZW sex determination system. The sex locus and sex-linked SNP markers were co-segregated in the center of the chromosome at a distance of 30.8 and 31.3 cm, respectively. This study presents sex-linked markers for MAS as well as valuable information about the sex chromosome and sex locus position in pistachio.

Biallelic Expression of Mucin-1 in Autosomal Dominant Tubulointerstitial Kidney Disease: Implications for Nongenetic Disease Recognition

Providing the correct diagnosis for patients with tubulointerstitial kidney disease and secondary degenerative disorders, such as hypertension, remains a challenge. The autosomal dominant tubulointerstitial kidney disease (ADTKD) subtype caused by MUC1 mutations (ADTKD-MUC1) is particularly difficult to diagnose, because the mutational hotspot is a complex repeat domain, inaccessible with routine sequencing techniques. Here, we further evaluated SNaPshot minisequencing as a technique for diagnosing ADTKD-MUC1 and assessed immunodetection of the disease-associated mucin 1 frameshift protein (MUC1-fs) as a nongenetic technique. We re-evaluated detection of MUC1 mutations by targeted repeat enrichment and SNaPshot minisequencing by haplotype reconstruction via microsatellite analysis in three independent ADTKD-MUC1 families. Additionally, we generated rabbit polyclonal antibodies against MUC1-fs and evaluated immunodetection of wild-type and mutated allele products in human kidney biopsy specimens. The detection of MUC1 mutations by SNaPshot minisequencing was robust. Immunostaining with our MUC1-fs antibodies and an MUC1 antibody showed that both proteins are readily detectable in human ADTKD-MUC1 kidneys, with mucin 1 localized to the apical membrane and MUC1-fs abundantly distributed throughout the cytoplasm. Notably, immunohistochemical analysis of MUC1-fs expression in clinical kidney samples facilitated reliable prediction of the disease status of individual patients. Diagnosing ADTKD-MUC1 by molecular genetics is possible, but it is technically demanding and labor intensive. However, immunohistochemistry on kidney biopsy specimens is feasible for nongenetic diagnosis of ADTKD-MUC1 and therefore, a valid method to select families for further diagnostics. Our data are compatible with the hypothesis that specific molecular effects of MUC1-fs underlie the pathogenesis of this disease.

Forensic genetic informativeness of an SNP panel consisting of 19 multi-allelic SNPs

Current research focusing on forensic personal identification, phenotype inference and ancestry information on single-nucleotide polymorphisms (SNPs) has been widely reported. In the present study, we focused on tetra-allelic SNPs in the Chinese Han population. A total of 48 tetra-allelic SNPs were screened out from the Chinese Han population of the 1000 Genomes Database, including Chinese Han in Beijing (CHB) and Chinese Han South (CHS). Considering the forensic genetic requirement for the polymorphisms, only 11 tetra-allelic SNPs with a heterozygosity >0.06 were selected for further multiplex panel construction. In order to meet the demands of personal identification and parentage identification, an additional 8 tri-allelic SNPs were combined into the final multiplex panel. To ensure application in the degraded DNA analysis, all the PCR products were designed to be 87–188 bp. Employing multiple PCR reactions and SNaPshot minisequencing, 511 unrelated Chinese Han individuals from Sichuan were genotyped. The combined match probability (CMP), combined discrimination power (CDP), and cumulative probability of exclusion (CPE) of the panel were 6.07 × 10−11, 0.9999999999393 and 0.996764, respectively. Based on the population data retrieved from the 1000 Genomes Project, Fst values between Chinese Han in Sichuan (SCH) and all the populations included in the 1000 Genomes Project were calculated. The results indicated that two SNPs in this panel may contain ancestry information and may be used as markers of forensic biogeographical ancestry inference.

Effect of a novel polymorphism of the LF and TLR4 genes on milk yield and milk compositions in dairy goats

In total 593 goats were genotyped on 5 single nucleotide polymorphisms (SNP): one SNP at Lactoferrin in exon 4 and four SNPs at Toll-like receptor 4 in exon 3 by using SNaPshot minisequencing. The most prevalent genotype was TT (546) in LF and genotype combination TTCCCCGC (216) and TTCCCCCC (204) in TLR4. There is possible influence of LF and TLR4 on milk yield and milk components, therefore, further studies are needed to evaluate this possible association in more number of goat farms.

Development and linkage mapping of novel sex-linked markers for marker-assisted cultivar breeding in pistachio (Pistacia vera L.)

The dioecious character of Pistacia vera L (the pistachio tree) limits its breeding capacity. Thus, early stage selection of males can save time, labor, and land. This study aimed to develop sex-linked single nucleotide polymorphism (SNP) markers, together with expressed sequence tag-derived simple sequence repeats (EST-SSRs), to determine position of the sex locus in pistachio by constructing a linkage map of its sex chromosome for the first time. Nine novel sex-linked SNP markers were successfully identified by SNaPshot minisequencing analysis of 25 SNP loci from 17 restriction site-associated DNA (RAD) reads in 309 individuals. All nine markers were heterozygous in females and homozygous in males supporting a ZW/ZZ sex determination system in pistachio. A total of 105 segregating SSRs and sex-linked markers were used to identify the sex chromosome and the position of the sex locus through analysis of a Siirt × Bagyolu F1 population with 122 progenies. Of these 105 markers, four common and four paternal SSRs were mapped onto the sex chromosome, along with the phenotypic sex locus and sex-linked markers. The resulting consensus map had a total length of 65.19 cM. The sex locus and sex-linked SNP markers were located in the center of the chromosome at a distance of 31.86 and 31.92 cM, respectively. This study presents valuable information about the sex chromosome and sex locus position as well as novel polymorphic EST-SSRs and nine sex-linked SNP markers in pistachio.

Rapid and Reliable Detection of Nonsyndromic Hearing Loss Mutations by Multicolor Melting Curve Analysis

Hearing loss is a common birth defect worldwide. The GJB2, SLC26A4, MT-RNR1 and MT-TS1 genes have been reported as major pathogenic genes in nonsyndromic hearing loss. Early genetic screening is recommended to minimize the incidence of hearing loss. We hereby described a multicolor melting curve analysis (MMCA)-based assay for simultaneous detection of 12 prevalent nonsyndromic hearing loss-related mutations. The three-reaction assay could process 30 samples within 2.5 h in a single run on a 96-well thermocycler. Allelic types of each mutation could be reproducibly obtained from 10 pg ~100 ng genomic DNA per reaction. For the mitochondrial mutations, 10% ~ 20% heteroplasmic mutations could be detected. A comparison study using 501 clinical samples showed that the MMCA assay had 100% concordance with both SNaPshot minisequencing and Sanger sequencing. We concluded that the MMCA assay is a rapid, convenient and cost-effective method for detecting the common mutations, and can be expectedly a reliable tool in preliminary screening of nonsyndromic hearing loss in the Chinese Han population.

Mapping SLCO1B1 Genetic Variation for Global Precision Medicine in Understudied Regions in Africa: A Focus on Zulu and Cape Admixed Populations.

The U.S. President Barack Obama has announced, in his State of the Union address on January 20, 2015, the Precision Medicine Initiative, a US$215-million program. For global precision medicine to become a reality, however, biological and environmental "variome" in previously understudied populations ought to be mapped and catalogued. Chief among the molecular targets that warrant global mapping is the organic anion-transporting polypeptide 1B1 (OATP1B1), encoded by solute carrier organic anion transporter family member 1B1 (SLCO1B1), a hepatic uptake transporter predominantly expressed in the basolateral side of hepatocytes. Human OATP1B1 plays a crucial role in the transport of a wide variety of substrates. This includes endogenous compounds such as bile salts as well as medicines, including benzylpenicillin, methotrexate, pravastatin, and rifampicin, and natural toxins microcystin and phalloidin. Genetic variations observed in the SLCO1B1 gene have been associated with altered in vitro and in vivo OATP1B1 transport activity, and consequently influencing patients' response to medicines, toxins, and susceptibility to common complex diseases. Well-characterized haplotypes, *5 (RS4149056C) and *15 (RS4149056T), have been associated with a strikingly reduced uptake of multiple OATP1B1 substrates, including estrone-3-sulfate, estradiol-17β-d-glucuronide, atorvastatin, cerivastatin, pravastatin, and rifampicin. In particular, RS4149056C is observed in 60% of the Cape admixed (CA) population and is associated with increased plasma concentrations of many statins as well as fexofenadine and repaglinide. We designed and optimized a SNaPshot minisequencing panel to characterize the variants of relevance for precision medicine in the clinic. We report here the first study on allele and genotype frequencies for 10 nonsynonymous, 4 synonymous, and 6 intronic single-nucleotide polymorphisms of SLCO1B1 in the Zulu and CA populations of South Africa. These variants are further contextualized here, in relation to their potential clinical relevance. These observations collectively contribute to current efforts to advance global precision medicine in understudied populations and resource-limited regions of the world.

CYP11B2 gene polymorphism and essential hypertension among Tibetan, Dongxiang and Han populations from northwest of China

ABSTRACTEssential hypertension (EH) is a complex multifactorial condition influenced by both genetic and environmental factors; aldosterone synthase (CYP11B2) is a key enzyme which involves in the terminal steps of aldosterone synthesis. The result of relationship between C-344T of CYP11B2 polymorphism and EH was controversial. This study was undertaken to investigate the association of C-344T polymorphism with EH in the populations of Tibetan, Dongxiang and Han from northwest of China. A total of 2115 participants aged 18–70 years were enrolled in this study. In total, 1776 blood samples, including 545 Tibetan (305 hypertensive and 240 normotensive), 530 Dongxiang (254 hypertensive and 276 normotensive) and 701 Han (338 hypertensive and 363 normotensive), were analyzed successfully by using Snapshot minisequencing method, 30 samples were also performed by direct sequencing (5 hypertensive and 5 normotensive in each population, respectively). The frequencies of genotype and allele of CYP11B2 (C-344T) were not significantly different between EH group and control group in every ethnic population (p > 0.05). However, in female population of Tibetan, the frequencies of CC and CT genotype and C allele in EH group were higher than in control (p < 0.05) group. The frequencies of CC genotype and C allele in both the normotensive controls and EH patients in Tibetan population were higher than in Dongxiang and Han populations. Our study suggests that there is lack of association between C-344T polymorphism of CYP11B2 gene and EH in Dongxiang and Han populations, whereas the polymorphism was correlated with EH in female population of Tibetan.

Angiotensinogen M235T, β2 Adrenergic Receptor Arg16Gly and Aldosterone Synthase C-344T Gene Polymorphisms and Essential Hypertension among Han Population Living at High Altitude in China

We explored the association of angiotensinogen (AGT) M235T, β2 adrenergic receptor (β2-AR) Arg16Gly and aldosterone synthase (CYP11B2) C-344T genes polymorphisms with essential hypertension (EH) in Han population living at high altitude in China. A total of 390 hypertensive subjects (males, 207; females, 183) and 424 normal healthy individuals (males, 251; females, 173) were enrolled in this study based on the inclusion and exclusion criteria. The polymorphisms of AGT M235T, β2-AR Arg16Gly, CYP11B2 C-344T genes were analyzed by Snapshot mini sequencing method. The frequencies of CC genotype and C allele of AGT M235T in EH group were higher than in control (p 0.05, respectively), in gender-specific analysis, the differences were also not found (p>0.05, respectively). This finding suggests that the polymorphism of AGT M235T was correlated with EH in Han population living at high altitude in China, however, β2-AR Arg16Gly and CYP11B2 C-344T polymorphism were unlikely to associated with hypertensive subjects of this population.