ABSTRACT
Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.
Subject(s)
DNA Methylation/genetics , Neanderthals/anatomy & histology , Neanderthals/genetics , Pan troglodytes/anatomy & histology , Pan troglodytes/genetics , Phenotype , Animals , Base Sequence , Databases, Genetic , Extinction, Biological , Fossils , Genome, Human/genetics , Humans , Polymorphism, Single Nucleotide/genetics , Skeleton , SkullABSTRACT
The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.
Subject(s)
Archaeology , Genome, Human/genetics , Genomics , Human Migration/history , Mummies/history , Phylogeny , Agriculture/history , Animals , Cattle , China , Cultural Characteristics , Dental Calculus/chemistry , Desert Climate , Diet/history , Europe , Female , Goats , Grassland , History, Ancient , Humans , Male , Milk Proteins/analysis , Phylogeography , Principal Component Analysis , Proteome/analysis , Proteomics , Sheep , Whole Genome SequencingABSTRACT
Periodontitis is a common inflammatory disease characterized by a complex etiology, which is the result of a combination of genetic and environmental factors. Genetic variants linked to the periodontitis disease were already investigated, however, little was known regarding the severity of this disease. Recently, long runs of homozygosity (ROH) were associated with several multifactorial diseases. Therefore, in our work, we tried to assess the role of ROH and periodontitis status. We found an association between the excess of homozygosity owing to ROH and staging of periodontitis. More in detail, the total amount of homozygosity owing to ROH is positively associated with an increased severity of periodontitis (P = 0.0001). Regression tree analysis showed the impact of ROH burden in discriminating individuals with mild periodontitis stages I and II and periodontitis stages III and IV (P < 0.001). Furthermore, ROH mapping highlights several regions associated with a severe status of periodontitis (odds ratio > 1). Among them, we found a total of 33 genes. Interestingly, some of these genes were previously associated with granulocyte or platelet measures, both linked to the onset and the progression of periodontal disease. Our results suggest the not only single variants association test could help to risk assessment but even individual genomic features; furthermore, our ROH mapping highlighted the possible role of multiple genes in periodontal development.
Subject(s)
Genetic Predisposition to Disease , Homozygote , Inflammation/genetics , Periodontitis/genetics , Adult , Female , Genetic Association Studies , Genome, Human/genetics , Genomics , Genotype , Humans , Inflammation/pathology , Male , Middle Aged , Periodontitis/classification , Periodontitis/pathology , Polymorphism, Single Nucleotide/geneticsABSTRACT
OBJECTIVES: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences. METHODS: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools. RESULTS: The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style. CONCLUSION: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.
Subject(s)
Human Migration/history , White People , Burial/history , Chromosomes, Human, Y/genetics , DNA, Ancient/analysis , DNA, Mitochondrial/genetics , Female , Genetics, Population , Genome, Human/genetics , History, Ancient , Humans , Male , Scandinavian and Nordic Countries/ethnology , Tooth/chemistry , White People/ethnology , White People/geneticsABSTRACT
BACKGROUND: Periodontitis is a common oral disease caused by host inflammatory response towards bacteria biofilm. The chronic activation of immune response leads to destruction of teeth supporting tissue, bone loss and tooth detachment. Different factors could be involved in the development and severity of the disease; among them the host genetic background should be considered. OBJECTIVES: In our study, we analysed haploblocks in a genomic region within major histocompatibility complex (MHC) locus aimed at disclosing a possible correlation with the risk of periodontal disease in 602 adult subjects from North-East Italy. RESULTS: The CTTAC haploblock (formed by LTA-rs2857709, LTA-rs2844484, LTA- rs2229094, LTA-rs2229092 and LTA-rs1041981 polymorphisms) correlated with protection towards periodontitis condition, after regression analysis including age and smoking status as covariates (P-value = 0.015). CONCLUSION: Our results suggest that a haplotype within LTA gene (encoding for lymphotoxin alpha) is involved in the susceptibility towards chronic periodontitis.
Subject(s)
Chronic Periodontitis/genetics , Genetic Association Studies , Genetic Predisposition to Disease/genetics , Genome, Human/genetics , Haploidy , Lymphotoxin-alpha/genetics , Major Histocompatibility Complex/genetics , Adult , Aged , Chronic Periodontitis/immunology , Chronic Periodontitis/microbiology , Female , Genetic Loci/genetics , Humans , Inflammation , Italy , Male , Middle Aged , Risk , Severity of Illness IndexABSTRACT
OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
Subject(s)
DNA, Ancient , Dental Calculus/chemistry , Dentin/chemistry , Genome, Human/genetics , Genomics/methods , Archaeology , DNA, Ancient/analysis , DNA, Ancient/isolation & purification , Dental Calculus/microbiology , Female , Humans , Male , Sequence Analysis, DNAABSTRACT
Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2: showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing.
Subject(s)
Alkylating Agents/chemistry , DNA/chemistry , Imidazoles/chemistry , Nylons/chemistry , Pyrroles/chemistry , Receptor, ErbB-2/genetics , Alkylation , Base Sequence , Genome, Human/genetics , High-Throughput Nucleotide Sequencing , Humans , Promoter Regions, Genetic/geneticsABSTRACT
Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly (MDMHB) is an autosomal-dominant bone dysplasia characterized by metaphyseal flaring of long bones, enlargement of the medial halves of the clavicles, maxillary hypoplasia, variable brachydactyly, and dystrophic teeth. We performed genome-wide SNP genotyping in five affected and four unaffected members of an extended family with MDMHB. Analysis for copy-number variations revealed that a 105 kb duplication within RUNX2 segregated with the MDMHB phenotype in a region with maximum linkage. Real-time PCR for copy-number variation in genomic DNA in eight samples, as well as sequence analysis of fibroblast cDNA from one subject with MDMHB confirmed that affected family members were heterozygous for the presence of an intragenic duplication encompassing exons 3 to 5 of RUNX2. These three exons code for the Q/A domain and the functionally essential DNA-binding runt domain of RUNX2. Transfection studies with murine Runx2 cDNA showed that cellular levels of mutated RUNX2 were markedly higher than those of wild-type RUNX2, suggesting that the RUNX2 duplication found in individuals with MDMHB leads to a gain of function. Until now, only loss-of-function mutations have been detected in RUNX2; the present report associates an apparent gain-of-function alteration of RUNX2 function with a distinct rare disease.
Subject(s)
Brachydactyly/genetics , Core Binding Factor Alpha 1 Subunit/genetics , Gene Duplication/genetics , Osteochondrodysplasias/genetics , Adolescent , Brachydactyly/diagnostic imaging , Chromosomes, Human, Pair 6/genetics , Exons/genetics , Facies , Family , Female , Fingers/abnormalities , Fingers/diagnostic imaging , Genome, Human/genetics , Humans , Male , Maxilla/abnormalities , Maxilla/diagnostic imaging , Osteochondrodysplasias/diagnostic imaging , Pedigree , Radiography , Young AdultABSTRACT
Oculoectodermal syndrome (OES) is a rare disease characterized by a combination of congenital scalp lesions and ocular dermoids, with additional manifestations including non-ossifying fibromas and giant cell granulomas of the jaw occurring during the first decade of life. To identify the genetic etiology of OES, we conducted whole-genome sequencing of several tissues in an affected individual. Comparison of DNA from a non-ossifying fibroma to blood-derived DNA allowed identification of a somatic missense alteration in KRAS NM_033360.3(KRAS):c.38G>A, resulting in p.Gly13Asp. This alteration was also observed in the patient's other affected tissues including the skin and muscle. Targeted sequencing in a second, unrelated OES patient identified an NM_033360.3(KRAS):c.57G>C, p.Leu19Phe alteration. Allelic frequencies fell below 40% in all tissues examined in both patients, suggesting that OES is a mosaic RAS-related disorder, or RASopathy. The characteristic findings in OES, including scalp lesions, ocular dermoids, and benign tumors, are found in other mosaic and germline RASopathies. This discovery also broadens our understanding of the spectrum of phenotypes resulting from KRAS alterations. Future research into disease progression with regard to malignancy risk and investigation of RAS-targeted therapies in OES is warranted. KRAS sequencing is clinically available and may also now improve OES diagnostic criteria.
Subject(s)
Dermoid Cyst/genetics , Dermoid Cyst/pathology , Ectodermal Dysplasia/genetics , Ectodermal Dysplasia/pathology , Genome, Human/genetics , Proto-Oncogene Proteins p21(ras)/genetics , Base Sequence , Child , Child, Preschool , Choristoma/pathology , Corneal Diseases/pathology , Female , Gene Frequency , Growth Disorders/pathology , Humans , Male , Molecular Sequence Data , Mutation, Missense/genetics , Scalp/pathology , Sequence Analysis, DNAABSTRACT
Chronic infection with hepatitis C virus (HCV) affects 170 million people worldwide and is the leading cause of cirrhosis in North America. Although the recommended treatment for chronic infection involves a 48-week course of peginterferon-alpha-2b (PegIFN-alpha-2b) or -alpha-2a (PegIFN-alpha-2a) combined with ribavirin (RBV), it is well known that many patients will not be cured by treatment, and that patients of European ancestry have a significantly higher probability of being cured than patients of African ancestry. In addition to limited efficacy, treatment is often poorly tolerated because of side effects that prevent some patients from completing therapy. For these reasons, identification of the determinants of response to treatment is a high priority. Here we report that a genetic polymorphism near the IL28B gene, encoding interferon-lambda-3 (IFN-lambda-3), is associated with an approximately twofold change in response to treatment, both among patients of European ancestry (P = 1.06 x 10(-25)) and African-Americans (P = 2.06 x 10(-3)). Because the genotype leading to better response is in substantially greater frequency in European than African populations, this genetic polymorphism also explains approximately half of the difference in response rates between African-Americans and patients of European ancestry.
Subject(s)
Genetic Variation/genetics , Hepacivirus/drug effects , Hepatitis C, Chronic/drug therapy , Hepatitis C, Chronic/genetics , Interferon-alpha/pharmacology , Interleukins/genetics , Polyethylene Glycols/pharmacology , Viral Load , Black or African American/genetics , Chromosomes, Human, Pair 19/genetics , Clinical Trials as Topic , Europe/ethnology , Asia, Eastern/ethnology , Gene Frequency , Genome, Human/genetics , Genome-Wide Association Study , Genotype , Hepatitis C, Chronic/ethnology , Hepatitis C, Chronic/virology , Hispanic or Latino/genetics , Humans , Interferon alpha-2 , Interferon-alpha/adverse effects , Interferon-alpha/therapeutic use , Interferons , Pharmacogenetics , Polyethylene Glycols/adverse effects , Polyethylene Glycols/therapeutic use , Polymorphism, Single Nucleotide/genetics , Recombinant ProteinsABSTRACT
INTRODUCTION: Attempts have been made to identify susceptibility genes of mandibular prognathism by genome-wide linkage studies, but the results of susceptibility loci are inconsistent. There has been no genome-wide association study of mandibular prognathism. Our objective was to perform a genome-wide association study using 23,465 microsatellite markers to detect mandibular prognathism susceptibility regions. METHODS: The study was based on the pooled DNA method, including 2 steps of screening on the whole genome and subsequent individual genotyping, with 240 experimental subjects and 360 control subjects from the Japanese population. RESULTS: Two suggestive associations on chromosomes 1q32.2 (D1S1358i: P = 4.22 × 10(-4)) and 1p22.3 (D1S0411i: P = 6.66 × 10(-4)) were shown, and PLXNA2 and SSX2IP were suggested to be candidate genes; 1p22.3 flanked the region indicated by previous linkage analysis. CONCLUSIONS: The results of the genome-wide association study showed that 2 loci (1q32.2 and 1p22.3) are likely to be susceptibility regions of mandibular prognathism: 1p32.2 is a novel locus, and identification of 1p22.3 supports the results of previous linkage analysis.
Subject(s)
Microsatellite Repeats/genetics , Prognathism/genetics , Adolescent , Adult , Chromosome Mapping , Chromosomes, Human, Pair 1/genetics , Gene Frequency/genetics , Genetic Linkage/genetics , Genetic Predisposition to Disease/genetics , Genome, Human/genetics , Genome-Wide Association Study , Genotype , Humans , Malocclusion, Angle Class III , Middle Aged , Neoplasm Proteins/genetics , Nerve Tissue Proteins/genetics , Receptors, Cell Surface/genetics , Repressor Proteins/genetics , Young AdultABSTRACT
Recent developments in high-throughput sequence capture methods and next-generation sequencing technologies have now made exome sequencing a viable approach to elucidate the genetic basis of Mendelian disorders with hitherto unknown etiology. In addition, exome sequencing is increasingly being employed as a diagnostic tool for specific genetic diseases, particularly in the context of those disorders characterized by significant genetic and phenotypic heterogeneity, for example, Charcot-Marie-Tooth disease and congenital disorders of glycosylation. Such disorders are challenging to interrogate with conventional polymerase chain reaction-Sanger sequencing methods, because of the inherent difficulty in prioritizing candidate genes for diagnostic testing. Here, we explore the value of exome sequencing as a diagnostic tool and discuss whether exome sequencing can come to serve a dual role in diagnosis and discovery. We summarize the current status of exome sequencing, the technical challenges facing it, and its adaptation to diagnostics, and make recommendations for the use of exome sequencing as a routine diagnostic tool. Finally, we discuss pertinent ethical concerns, such as the use of exome sequencing data, originally generated in a diagnostic context, in research investigations.
Subject(s)
Exome/genetics , Gene Targeting/methods , Gene Targeting/trends , Sequence Analysis, DNA/methods , Sequence Analysis, DNA/trends , Animals , Charcot-Marie-Tooth Disease/diagnosis , Charcot-Marie-Tooth Disease/genetics , Gene Targeting/ethics , Genome, Human/genetics , Humans , Sequence Analysis, DNA/ethicsABSTRACT
A single-step concentration and elution method is developed for detection of DNA in buffer, saliva, and blood. A nanotip capturing DNA using an electric field and capillary action is directly dissolved in buffer for qPCR analysis. The concentration yield and the relative parameters are compared with those of a commercial kit.
Subject(s)
Analytic Sample Preparation Methods/methods , DNA/genetics , DNA/isolation & purification , Nanotechnology/methods , Polymerase Chain Reaction/methods , Bacteriophage lambda/genetics , Carbon Compounds, Inorganic/chemistry , DNA/analysis , DNA/blood , DNA, Viral/analysis , DNA, Viral/genetics , Genome, Human/genetics , Humans , Nanowires/chemistry , Saliva/chemistry , Silicon Compounds/chemistry , Time FactorsABSTRACT
This study explored the role of TCOF1 insertion mutations in Taiwanese patients with craniofacial anomalies. Twelve patients with single or multiple, asymmetrical congenital craniofacial anomalies were enrolled. Genomic DNA was prepared from leukocytes; the coding regions of TCOF1 were analyzed by polymerase chain reaction and direct sequencing. Clinical manifestations were correlated to the TCOF1 mutation. Six of 12 patients diagnosed with hemifacial microsomia exhibited a novel insertion mutation 4127 ins G (frameshift) in exon 24 in the TCOF1 gene. All six patients were diagnosed with anomalies on the left side. In addition, four of these six patients had hearing impairment; three had other major anomalies; and two had developmental delay. The insertion caused a frameshift, an early truncation, the loss of two putative nuclear localization signals (residues 1404-1420 and 1424-1440), and the loss of coiled coil domain (1406-1426) in treacle protein. These findings support the existence of two regulators of growth of the mandibular condyles.
Subject(s)
Facial Asymmetry/genetics , Mutagenesis, Insertional , Nuclear Proteins/genetics , Phosphoproteins/genetics , Adult , Child , Child, Preschool , Craniofacial Abnormalities/genetics , Craniofacial Abnormalities/pathology , Exons , Female , Frameshift Mutation , Genome, Human/genetics , Humans , Infant , Infant, Newborn , Male , Nuclear Localization Signals/genetics , Nuclear Proteins/metabolism , Phenotype , Phosphoproteins/metabolism , Polymorphism, Single Nucleotide , Sequence Analysis, DNA , TaiwanABSTRACT
BACKGROUND: The non-invasive, flexible and easy sample collection makes saliva an interesting source of DNA for research and diagnostic purposes. The aim of our study was to find the most suitable collection method for biological material from the oral cavity and the most effective DNA isolation technique for further analytic applications. METHODS: DNA was isolated from swabs, Salivette saliva, whole saliva and samples collected with a commercial set for scraping of buccal cells. Phenol-chloroform extraction and isolation using a silica membrane based commercial kit were compared. Quantity of bacterial and human genomic DNA was estimated using real time PCR. The effects of storage conditions on DNA recovery were assessed. RESULTS: Sample collection techniques significantly affected the quantity of DNA for both, silica membrane based and phenol-chloroform isolations. Whole saliva provided the largest number of bacterial and human genome copies after both extraction methods. Storage for 36 months at 20°C reduced recovery of human genomic DNA five times after silica membrane based extraction and 10 times after phenol-chloroform isolation. CONCLUSIONS: Whole saliva was found to be the most suitable material for human and bacterial DNA isolation. Both compared methods are useful considering the quantity of extracted DNA.
Subject(s)
DNA/isolation & purification , Saliva/chemistry , Specimen Handling/methods , Adult , DNA/analysis , Genome, Human/genetics , Humans , Young AdultABSTRACT
The addition of genomic information to our understanding of oral disease is driving important changes in oral health care. It is anticipated that genome-derived information will promote a deeper understanding of disease etiology and permit earlier diagnosis, allowing for preventative measures prior to disease onset rather than treatment that attempts to repair the diseased state. Advances in genome technologies have fueled expectations for this proactive healthcare approach. Application of genomic testing is expanding and has already begun to find its way into the practice of clinical dentistry. To take full advantage of the information and technologies currently available, it is vital that dental care providers, consumers, and policymakers be aware of genomic approaches to understanding of oral diseases and the application of genomic testing to disease diagnosis and treatment. Ethical, legal, clinical, and educational initiatives are also required to responsibly incorporate genomic information into the practice of dentistry. This article provides an overview of the application of genomic technologies to oral health care and introduces issues that require consideration if we are to realize the full potential of genomics to enable the practice of personalized dental medicine.
Subject(s)
Dental Care , Genome, Human/genetics , Personal Health Services , Precision Medicine , Computational Biology , Genetic Techniques , Genetic Testing , Humans , Mouth Diseases/genetics , Mouth Diseases/prevention & control , Tooth Diseases/genetics , Tooth Diseases/prevention & controlABSTRACT
OBJECTIVE: The aim of the study was to examine whether the MBL2 C(-290)G and G161A, MASP2 A359G, AMELX C287T and C522T, and ENAM C2452T polymorphisms are associated with dental caries. SUBJECTS AND METHODS: Genomic DNA of 95 Polish children with 'higher caries experience' (HC) and 84 subjects with 'lower caries experience' (LC) belonging to two age-groups (5 and 13 years old) was extracted from the buccal mucosa. SNPs were genotyped with PCR-RFLP methods. RESULTS: Among 5-year-old children, we found significantly higher percentage of subjects carrying MBL2 (-290)G allele in HC group compared with LC group (43.2%vs 17.6%, P = 0.023). MBL2 C(-290)G-G161A C-G haplotype was overrepresented in LC group in 5-year-olds (P = 0.01), while the opposite association was observed in 13-year-olds, where C-G was overrepresented in HC group (P = 0.028). In 5-year-old children, the frequency of MBL2 G-G haplotype was higher in HC group compared with LC subjects (P = 0.045), while the opposite association (with borderline significance) was observed in 13-year-old children (P = 0.057). SNPs in MASP2, AMELX, and ENAM were not associated with dental caries. CONCLUSION: MBL2 gene polymorphism is associated with caries experience in Polish children, but the direction of this association seems to be opposite in primary and permanent dentition.
Subject(s)
Amelogenin/genetics , Dental Caries/genetics , Mannose-Binding Lectin/genetics , Mannose-Binding Protein-Associated Serine Proteases/genetics , Polymorphism, Single Nucleotide/genetics , Proteins/genetics , Adenine , Adolescent , Alleles , Case-Control Studies , Child, Preschool , Cytosine , DMF Index , Extracellular Matrix Proteins , Female , Gene Frequency/genetics , Genome, Human/genetics , Guanine , Haplotypes/genetics , Heterozygote , Humans , Male , Mutation/genetics , Poland , ThymineABSTRACT
Complementary DNA (cDNA) is valuable for investigating protein structure and function in the study of life science, but it is difficult to obtain by traditional reverse transcription. We employed a novel strategy to clone human leukemia inhibitory factor (hLIF) gene cDNA from genomic DNA, which was directly isolated from the mucous membrane of mouth. The hLIF sequence, which is 609 bp long and is composed of three exons, can be acquired within a few hours by amplifying each exon and splicing all of them using overlap-PCR. This new approach developed is simple, time- and cost-effective, without RNA preparation or cDNA synthesis, and is not limited to the specific tissues for a particular gene and the expression level of the gene.
Subject(s)
Cloning, Molecular/methods , DNA, Complementary/genetics , DNA, Complementary/isolation & purification , Genome, Human/genetics , Leukemia Inhibitory Factor/genetics , Mouth Mucosa/metabolism , Amino Acid Sequence , Base Sequence , Exons/genetics , Humans , Leukemia Inhibitory Factor/chemistry , Molecular Sequence Data , Open Reading Frames/genetics , RNA Splicing/genetics , Reverse Transcriptase Polymerase Chain ReactionABSTRACT
We have explored the potential role of genetics in the development of osteonecrosis of the jaw (ONJ) in multiple myeloma (MM) patients under bisphosphonate therapy. A genome-wide association study was performed using 500 568 single nucleotide polymorphisms (SNPs) in 2 series of homogeneously treated MM patients, one with ONJ (22 MM cases) and another without ONJ (65 matched MM controls). Four SNPs (rs1934951, rs1934980, rs1341162, and rs17110453) mapped within the cytochrome P450-2C gene (CYP2C8) showed a different distribution between cases and controls with statistically significant differences (P = 1.07 x 10(-6), P = 4.231 x 10(-6), P = 6.22 x 10(-6), and P = 2.15 x 10(-6), respectively). SNP rs1934951 was significantly associated with a higher risk of ONJ development even after Bonferroni correction (P corrected value = .02). Genotyping results displayed an overrepresentation of the T allele in cases compared with controls (48% vs 12%). Thus, individuals homozygous for the T allele had an increased likelihood of developing ONJ (odds ratio 12.75, 95% confidence interval 3.7-43.5).
Subject(s)
Aryl Hydrocarbon Hydroxylases/genetics , Diphosphonates/adverse effects , Genome, Human/genetics , Jaw Diseases/genetics , Multiple Myeloma/complications , Osteonecrosis/genetics , Polymorphism, Single Nucleotide/genetics , Alleles , Cytochrome P-450 CYP2C8 , Diphosphonates/therapeutic use , Genetic Predisposition to Disease , Haplotypes , Humans , Jaw Diseases/chemically induced , Jaw Diseases/complications , Jaw Diseases/enzymology , Multiple Myeloma/drug therapy , Multiple Myeloma/enzymology , Multiple Myeloma/genetics , Osteonecrosis/chemically induced , Osteonecrosis/complications , Osteonecrosis/enzymologyABSTRACT
Genomic disorders have been increasingly recognized as a significant source of clinically relevant phenotypes largely fostered by advances in technologies for genome-wide analyses. Molecular and clinical studies of copy number variants involving chromosome 17 began with locus-specific studies of Charcot-Marie-Tooth disease type 1A (CMT1A, OMIM #118220) and hereditary neuropathy with liability to pressure palsies (HNPP, OMIM #162500), which laid the foundation for the paradigm of duplication/deletion and gene-dosage for our understanding of genomic disorders. With the clinical introduction of high-resolution array comparative genomic hybridization (aCGH) the number of recognized genomic disorders including microduplications has been increasing rapidly. A relatively high proportion of disease-associated copy number variants map to chromosome 17. This may result from its unique structural features, such as relative abundance of segmental duplications and interspersed repetitive elements, high gene content, and the presence of dosage-sensitive genes. These genomic rearrangements are mediated by diverse mechanisms including Non-Allelic Homologous Recombination (NAHR), Non-Homologous End-Joining (NHEJ), and Fork Stalling and Template Switching (FoSTeS). We provide specific examples of chromosome 17 microduplications with the emphasis on their phenotype, specific clinical features aiding in their diagnosis, and counseling.