Genomic analyses of patients with unexplained early onset scoliosis.
Spine Deform. 2014 Sep 1;2(5):324-332
Authors: Gao X, Gotway G, Rathjen K, Johnston C, Sparagana S, Wise CA
STUDY DESIGN: To test for rare genetic mutations, a cohort of patients with unexplained early onset scoliosis (EOS) was screened using high-density microarray genotyping. A cohort of patients with adolescent idiopathic scoliosis (AIS) was similarly screened, and the results were compared.
SUMMARY OF BACKGROUND DATA: Patients with scoliosis in infancy or early childhood (EOS) are at high risk for progressive deformity and associated problems including respiratory compromise. EOS is frequently associated with genetic disorders, but many patients present with non-specific clinical features and without an associated diagnosis. We hypothesized that EOS in these patients may be caused by rare genetic mutations detectable by next-generation genomic methods.
METHODS: We ascertained 24 patients with unexplained EOS from pediatric orthopedic clinics. We genotyped them, along with 39 connecting family members, using the Illumina OmniExpress-12 v1.0 beadchip. Resulting genotypes were analyzed for chromosomal changes, specifically copy number variation (CNV) and absence of heterozygosity (AOH). We screened 482 AIS patients and 744 healthy controls, which were similarly genotyped with the same beadchip, for chromosomal changes identified in the EOS cohort.
RESULTS: Copy number variation (CNV) and absence of heterozygosity (AOH) analyses revealed a genetic diagnosis of chromosome 15q24 microdeletion syndrome in one patient, and maternal uniparental disomy of chromosome 14 in a second patient. Prior genetic testing and clinical evaluations had been negative in both cases. A large novel chromosome 10 deletion was likely causal in a third EOS patient. These mutations identified in the EOS patients were absent in AIS patients and controls, and thus not associated with AIS or found in asymptomatic individuals.
CONCLUSIONS: Our data underscore the utility of updated genetic evaluations including high-density microarray-based genotyping and other "next-generation" methods in patients with unexplained EOS, even where prior genetic studies were negative. These data also suggest the intriguing possibility that other mutations detectable by whole genome sequencing, as well as epigenetic effects, await discovery in the EOS population.
PMID: 25401082 [PubMed - as supplied by publisher]
Single-Nucleotide Polymorphism Discrimination Using High-Resolution Melting Analysis for the Genotyping of Bacillus anthracis.
Methods Mol Biol. 2015;1247:361-71
Authors: Derzelle S
High-resolution melting (HRM) is a post-PCR technique that determines with high precision the melt profile of PCR products using a new generation of double-stranded DNA-binding dyes and accurate fluorescence data acquisition over small temperature increments. The method can be used to interrogate small sets of single-nucleotide polymorphisms (SNPs). Here, we describe a simple and cost-effective HRM-based method for the screening of 14 phylogenetically informative SNPs within the genome of Bacillus anthracis that subtype the species into 13 major sublineages or subgroups. Fourteen monoplex and seven duplex SNP-discrimination assays have been designed. We detail the parameters most important for the successful application of HRM for B. anthracis genotyping.
PMID: 25399109 [PubMed - in process]
Intronic Variants in the NFKB1 Gene May Influence Hearing Forecast in Patients with Unilateral Sensorineural Hearing Loss in Meniere's Disease.
PLoS One. 2014;9(11):e112171
Authors: Cabrera S, Sanchez E, Requena T, Martinez-Bueno M, Benitez J, Perez N, Trinidad G, Soto-Varela A, Santos-Perez S, Martin-Sanz E, Fraile J, Perez P, Alarcon-Riquelme ME, Batuecas A, Espinosa-Sanchez JM, Aran I, Lopez-Escamez JA
Meniere's disease is an episodic vestibular syndrome associated with sensorineural hearing loss (SNHL) and tinnitus. Patients with MD have an elevated prevalence of several autoimmune diseases (rheumatoid arthritis, systemic lupus erythematosus, ankylosing spondylitis and psoriasis), which suggests a shared autoimmune background. Functional variants of several genes involved in the NF-κB pathway, such as REL, TNFAIP3, NFKB1 and TNIP1, have been associated with two or more immune-mediated diseases and allelic variations in the TLR10 gene may influence bilateral affectation and clinical course in MD. We have genotyped 716 cases of MD and 1628 controls by using the ImmunoChip, a high-density genotyping array containing 186 autoimmune loci, to explore the association of immune system related-loci with sporadic MD. Although no single nucleotide polymorphism (SNP) reached a genome-wide significant association (p<10-8), we selected allelic variants in the NF-kB pathway for further analyses to evaluate the impact of these SNPs in the clinical outcome of MD in our cohort. None of the selected SNPs increased susceptibility for MD in patients with uni or bilateral SNHL. However, two potential regulatory variants in the NFKB1 gene (rs3774937 and rs4648011) were associated with a faster hearing loss progression in patients with unilateral SNHL. So, individuals with unilateral MD carrying the C allele in rs3774937 or G allele in rs4648011 had a shorter mean time to reach hearing stage 3 (>40 dB HL) (log-rank test, corrected p values were p = 0.009 for rs3774937 and p = 0.003 for rs4648011, respectively). No variants influenced hearing in bilateral MD. Our data support that the allelic variants rs3774937 and rs4648011 can modify hearing outcome in patients with MD and unilateral SNHL.
PMID: 25397881 [PubMed - as supplied by publisher]
Serum microRNAs; miR-30c-5p, miR-223-3p, miR-302c-3p and miR-17-5p could be used as novel non-invasive biomarkers for HCV-positive cirrhosis and hepatocellular carcinoma.
Mol Biol Rep. 2014 Nov 13;
Authors: Oksuz Z, Serin MS, Kaplan E, Dogen A, Tezcan S, Aslan G, Emekdas G, Sezgin O, Altintas E, Tiftik EN
Recently, serum miRNAs have been evolved as possible biomarkers for different diseases including hepatocellular carcinoma and other types of cancers. Investigating certain serum miRNAs as novel non-invasive markers for early detection of HCV-positive cirrhosis and hepatocellular carcinoma (HCC). The expression profiles of 58 miRNA were analyzed in patient's plasma of chronic hepatitis C (CHC), HCV-positive cirrhosis and HCV-positive HCC and compared with control group samples. Totally 94 plasma samples; 64 patient plasma (26 CHC, 30 HCV-positive cirrhosis, 8 HCV-positive HCC) and 28 control group plasma, were included. The expression profiles of 58 miRNAs were detected for all patient and control group plasma samples by qRT-PCR using BioMarkTM 96.96 Dynamic Array (Fluidigm Corporation) system. In CHC group, expression profiles of miR-30a-5p, miR-30c-5p, miR-206 and miR-302c-3p were found significantly deregulated (p < 0.05) when compared versus control group. In HCV-positive cirrhosis group, expression profiles of miR-30c-5p, miR-223-3p, miR-302c-3p, miR-17-5p, miR-130a-3p, miR-93-5p, miR-302c-5p and miR-223-3p were found significantly deregulated (p < 0.05). In HCV-positive HCC group, expression profiles of miR-17-5p, miR-223-3p and miR-24-3p were found significant (p < 0.05). When all groups were compared versus control, miR-30c-5p, miR-223-3p, miR-302c-3p and miR-17-5p were found significantly deregulated for cirrhosis and HCC. These results imply that miR-30c-5p, miR-223-3p, miR-302c-3p and miR-17-5p could be used as novel non-invasive biomarkers of HCV-positive HCC in very early, even at cirrhosis stage of liver disease.
PMID: 25391771 [PubMed - as supplied by publisher]